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
AGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA  >  NZ_CP009273/3179174‑3179368
                                                                                                 |                                                                                                 
AGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACC                                                                                                 <  SRR3722077.1082170/100‑1 (MQ=60)
    ACTTTAGGGACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCC                                                                                             >  SRR3722077.204496/1‑100 (MQ=60)
    ACCTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCC                                                                                             <  SRR3722077.625830/100‑1 (MQ=60)
     CTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCC                                                                                            >  SRR3722077.528350/1‑100 (MQ=60)
                      GTAATTACGTTCAACAATACCAACAGCTATCAGGAACTAAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTC                                                                           >  SRR3722077.150571/1‑100 (MQ=60)
                          gagatggccgtgggtctcgtgggctcggagatgtgtataagagacagCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGC                                                                       <  SRR3722077.602739/53‑1 (MQ=60)
                                    CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG                                                             <  SRR3722077.807082/100‑1 (MQ=60)
                                    CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGAAACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG                                                             <  SRR3722077.935729/100‑1 (MQ=60)
                                     AATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGA                                                            >  SRR3722077.325946/1‑100 (MQ=60)
                                      ATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT                                                           <  SRR3722077.603422/100‑1 (MQ=60)
                                       TACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATT                                                          >  SRR3722077.1003060/1‑100 (MQ=60)
                                             CAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTAC                                                    >  SRR3722077.647642/1‑100 (MQ=60)
                                             CAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTAC                                                    >  SRR3722077.782933/1‑100 (MQ=60)
                                               GCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGA                                                  >  SRR3722077.1097004/1‑100 (MQ=60)
                                                CTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAG                                                 >  SRR3722077.33950/1‑100 (MQ=60)
                                                 TATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGT                                                <  SRR3722077.123622/100‑1 (MQ=60)
                                                  ATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGA‑TGCTTACGAGTAA                                              >  SRR3722077.14147/1‑100 (MQ=60)
                                                    CAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAAT                                             <  SRR3722077.98959/100‑1 (MQ=60)
                                                            GAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTG                                     >  SRR3722077.262016/1‑100 (MQ=60)
                                                               TTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCC                                  <  SRR3722077.505477/100‑1 (MQ=60)
                                                                      GCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCG                           >  SRR3722077.984382/1‑100 (MQ=60)
                                                                         CGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCC                        >  SRR3722077.198717/1‑100 (MQ=60)
                                                                         CGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCC                        <  SRR3722077.196832/100‑1 (MQ=60)
                                                                                   CCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTATAAGATTGCTTACGAGTAATCGCATTTGGCCtgtctcttatacacatctcc              >  SRR3722077.683600/1‑80 (MQ=60)
                                                                                   CCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCA              >  SRR3722077.878001/1‑100 (MQ=60)
                                                                                        agacagGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAAC         <  SRR3722077.760880/94‑1 (MQ=60)
                                                                                        AGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAAC         <  SRR3722077.27793/100‑1 (MQ=60)
                                                                                          CAAAGATGCCCCCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGG       <  SRR3722077.1152158/100‑1 (MQ=60)
                                                                                          CAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGG       <  SRR3722077.200490/100‑1 (MQ=60)
                                                                                           AAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTctgtctcttatacacatctccgag      >  SRR3722077.1129964/1‑76 (MQ=60)
                                                                                               ATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA  >  SRR3722077.1048050/1‑100 (MQ=60)
                                                                                                 |                                                                                                 
AGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA  >  NZ_CP009273/3179174‑3179368

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑