Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A3 F11 I1 R1 56 79.5 3383150 98.4% 3329019 146.6

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCA  >  NC_002947_CJ‑RC/278599‑278888
                                                                                                                                                  |                                                                                                                                                
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AAacccc                                                                                                                                             >  NB501016:282:H2V7GAFX2:1:11301:3105:17351/1‑146 (MQ=60)
             CGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCC                                                                                                                                               >  NB501016:282:H2V7GAFX2:3:21608:20141:18079/1‑137 (MQ=60)
                GACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCC                                                                                                                              <  NB501016:282:H2V7GAFX2:1:21205:1274:15431/151‑1 (MQ=60)
                CACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCC                                                                                                                              <  NB501016:282:H2V7GAFX2:1:21206:26692:15430/151‑1 (MQ=60)
                 ACAGACGTGTTCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCT                                                                                                                             <  NB501016:282:H2V7GAFX2:3:21603:18312:4509/151‑1 (MQ=60)
                   AGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCA                                                                                                                           <  NB501016:282:H2V7GAFX2:4:11501:1546:11151/151‑1 (MQ=60)
                            CTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCC                                                                                                                                          >  NB501016:282:H2V7GAFX2:3:21610:11231:8988/1‑127 (MQ=60)
                                            GTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGT                                                                                                  <  NB501016:282:H2V7GAFX2:4:21602:12129:8939/151‑1 (MQ=60)
                                                                                                                     TACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCG                                                                                                     >  NB501016:282:H2V7GAFX2:3:21407:9722:1055/1‑75 (MQ=60)
                                                                                                                                       TTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGG                                                                                                   <  NB501016:282:H2V7GAFX2:3:11601:10203:10484/59‑1 (MQ=60)
                                                                                                                                             GGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCA  >  NB501016:282:H2V7GAFX2:1:11210:24006:10862/1‑150 (MQ=60)
                                                                                                                                                  |                                                                                                                                                
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCA  >  NC_002947_CJ‑RC/278599‑278888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑