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
A1 F2 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCAG  >  NZ_CP009273/3579069‑3579265
                                                                                                   |                                                                                                 
GCTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATT                                                                                                   >  SRR3722077.717861/1‑100 (MQ=60)
 ccgtgggtctcgtgggctcggagatgtgtataagagacagGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCC                                                                                                  <  SRR3722077.150011/60‑1 (MQ=60)
 CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCC                                                                                                  <  SRR3722077.732971/100‑1 (MQ=60)
 CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCC                                                                                                  <  SRR3722077.694883/100‑1 (MQ=60)
                    acaGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG                                                                               <  SRR3722077.125087/97‑1 (MQ=60)
                    ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCG                                                                               <  SRR3722077.701650/100‑1 (MQ=60)
                        GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATT                                                                           >  SRR3722077.17351/1‑100 (MQ=60)
                          ggtctcgtgggctcggagatgtgtataagagacagGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTC                                                                         <  SRR3722077.276190/65‑1 (MQ=60)
                               ATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGC                                                                    <  SRR3722077.581729/100‑1 (MQ=60)
                                   GGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCT                                                                >  SRR3722077.293567/1‑100 (MQ=60)
                                   GGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCT                                                                >  SRR3722077.840039/1‑100 (MQ=60)
                                   GGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCT                                                                >  SRR3722077.748639/1‑100 (MQ=60)
                                   GGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCT                                                                >  SRR3722077.390509/1‑100 (MQ=60)
                                    GCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTG                                                               >  SRR3722077.786751/1‑100 (MQ=60)
                                         GGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATG                                                          <  SRR3722077.988221/100‑1 (MQ=60)
                                          GCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGA                                                         <  SRR3722077.505444/100‑1 (MQ=60)
                                            TTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATT                                                       <  SRR3722077.211463/100‑1 (MQ=60)
                                             TTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTT                                                      >  SRR3722077.688887/1‑100 (MQ=60)
                                                 TGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCAT                                                  <  SRR3722077.626641/100‑1 (MQ=60)
                                                              CCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTG                                     >  SRR3722077.344525/1‑100 (MQ=60)
                                                              CCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTG                                     >  SRR3722077.894562/1‑100 (MQ=60)
                                                                tctcgtgggctcggagatgtgcataagagacagATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCC                                   <  SRR3722077.425702/67‑1 (MQ=60)
                                                                     ACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGC                              >  SRR3722077.233947/1‑100 (MQ=60)
                                                                      CTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCC                             <  SRR3722077.862812/100‑1 (MQ=60)
                                                                          GACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTAT                         >  SRR3722077.124074/1‑100 (MQ=60)
                                                                              AAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCT                     >  SRR3722077.730814/1‑100 (MQ=60)
                                                                               AATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTT                    <  SRR3722077.645644/100‑1 (MQ=60)
                                                                                ATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTC                   <  SRR3722077.1005775/100‑1 (MQ=60)
                                                                                ATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTC                   <  SRR3722077.1032753/100‑1 (MQ=60)
                                                                                            AAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCctgtctcttata       >  SRR3722077.1133244/1‑88 (MQ=60)
                                                                                              GATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTC     >  SRR3722077.747104/1‑100 (MQ=60)
                                                                                              GATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTC     >  SRR3722077.952437/1‑100 (MQ=60)
                                                                                                 ATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCAG  <  SRR3722077.1127636/100‑1 (MQ=60)
                                                                                                   |                                                                                                 
GCTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCAG  >  NZ_CP009273/3579069‑3579265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑