Warning: skipping mate #1 of read '35177/1 reference=SEQUENCE845 position=981..981 description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '35177/1 reference=SEQUENCE845 position=981..981 description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '56981/2 reference=SEQUENCE103 position=complement(1..1) description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '56981/2 reference=SEQUENCE103 position=complement(1..1) description="reverse=True"' because it was < 2 characters long Warning: skipping mate #1 of read '67127/1 reference=SEQUENCE643 position=650..650 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '67127/1 reference=SEQUENCE643 position=650..650 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '86640/2 reference=SEQUENCE256 position=265..265 description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '86640/2 reference=SEQUENCE256 position=265..265 description="reverse=False"' because it was < 2 characters long Warning: skipping mate #1 of read '95355/1 reference=SEQUENCE837 position=470..470 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '95355/1 reference=SEQUENCE837 position=470..470 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #1 of read '100001/1 reference=SEQUENCE103 position=698..698 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '100001/1 reference=SEQUENCE103 position=698..698 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '184685/2 reference=SEQUENCE788 position=590..590 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '184685/2 reference=SEQUENCE788 position=590..590 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '216664/2 reference=SEQUENCE455 position=1107..1107 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '216664/2 reference=SEQUENCE455 position=1107..1107 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '217940/2 reference=SEQUENCE851 position=768..768 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '217940/2 reference=SEQUENCE851 position=768..768 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '232090/2 reference=SEQUENCE356 position=complement(1..1) description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '232090/2 reference=SEQUENCE356 position=complement(1..1) description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '237662/2 reference=SEQUENCE298 position=757..757 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '237662/2 reference=SEQUENCE298 position=757..757 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #2 of read '238155/2 reference=SEQUENCE173 position=1221..1221 description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '238155/2 reference=SEQUENCE173 position=1221..1221 description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '324523/2 reference=SEQUENCE751 position=complement(1..1) description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '324523/2 reference=SEQUENCE751 position=complement(1..1) description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '337201/2 reference=SEQUENCE696 position=1239..1239 description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '337201/2 reference=SEQUENCE696 position=1239..1239 description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '344508/2 reference=SEQUENCE398 position=complement(1..1) description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '344508/2 reference=SEQUENCE398 position=complement(1..1) description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '389524/2 reference=SEQUENCE329 position=557..557 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '389524/2 reference=SEQUENCE329 position=557..557 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #1 of read '394268/1 reference=SEQUENCE533 position=1202..1202 description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '394268/1 reference=SEQUENCE533 position=1202..1202 description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '423317/2 reference=SEQUENCE467 position=488..488 description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '423317/2 reference=SEQUENCE467 position=488..488 description="reverse=True"' because it was < 2 characters long Warning: skipping mate #1 of read '428504/1 reference=SEQUENCE634 position=complement(1..1) description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '428504/1 reference=SEQUENCE634 position=complement(1..1) description="reverse=False"' because it was < 2 characters long Warning: skipping mate #2 of read '437060/2 reference=SEQUENCE434 position=complement(1..1) description="reverse=True"' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read '437060/2 reference=SEQUENCE434 position=complement(1..1) description="reverse=True"' because it was < 2 characters long Warning: skipping mate #1 of read '491757/1 reference=SEQUENCE498 position=complement(1..1) description="reverse=False"' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read '491757/1 reference=SEQUENCE498 position=complement(1..1) description="reverse=False"' because it was < 2 characters long 500000 reads; of these: 500000 (100.00%) were paired; of these: 29464 (5.89%) aligned concordantly 0 times 291599 (58.32%) aligned concordantly exactly 1 time 178937 (35.79%) aligned concordantly >1 times ---- 29464 pairs aligned concordantly 0 times; of these: 8262 (28.04%) aligned discordantly 1 time ---- 21202 pairs aligned 0 times concordantly or discordantly; of these: 42404 mates make up the pairs; of these: 1740 (4.10%) aligned 0 times 15705 (37.04%) aligned exactly 1 time 24959 (58.86%) aligned >1 times 99.83% overall alignment rate