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 F50 I1 R2 870 341.9 11209456 97.2% 10895591 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP025268 3,652,831 A→G intergenic (+107/+38) CXP41_RS19090 → / ← CXP41_RS19095 hypothetical protein/IS5‑like element IS5 family transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0252683,652,8310AG100.0% 89.1 / NA 33intergenic (+107/+38)CXP41_RS19090/CXP41_RS19095hypothetical protein/IS5‑like element IS5 family transposase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/6);  total (27/6)

TAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAA  >  NZ_CP025268/3652694‑3652851
                                                                                                                                         |                    
tAATATAAATTTCACTGACGCAAATGTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAc                    >  2:1650029/1‑140 (MQ=255)
 aaTATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAGTTAGAcc                   >  2:3079581/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:680410/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:3493011/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:1262013/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:5442468/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:5337583/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:3943502/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:4333819/1‑140 (MQ=255)
   tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 <  1:2325560/140‑1 (MQ=255)
      aaaTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttc              >  1:3977643/1‑140 (MQ=255)
      aaaTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATATTTAAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttc              >  1:3977382/1‑140 (MQ=255)
        aTTTCAGTGAAGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGGTGAGGCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTGCCGTAGAAGCCTGGAATGAGCCTATGTAGACCGTgtctt            >  2:3712671/1‑140 (MQ=11)
        aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAGTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:3363208/1‑140 (MQ=255)
        aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  1:3003183/1‑140 (MQ=255)
        aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:4918646/1‑140 (MQ=255)
        aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:3520269/1‑140 (MQ=255)
         tttCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTCGAATCAGCCTATTTAGACCGTttcttc           <  2:4111476/140‑1 (MQ=255)
           tCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGc         <  1:3988086/140‑1 (MQ=37)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCGTTGAATCAGCCTATTTAGACCGTTTTTTCGCCa       >  2:3768329/1‑140 (MQ=255)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  2:5146343/1‑140 (MQ=25)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:153638/1‑140 (MQ=25)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  2:2298507/1‑140 (MQ=25)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:2446862/1‑140 (MQ=25)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:1464531/1‑140 (MQ=25)
             aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTCAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGccc       >  1:3115274/1‑139 (MQ=255)
             aCTGACGCAAATTGAGGGAATGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTGATTTCTTCATGTTTGAGTCGATTTTTTCTCCCGTAAATGCCTTGTATCCTCCTATTTAGACCGTTTCTTCGCCa       >  2:5226339/1‑140 (MQ=11)
                 aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   <  1:77977/140‑1 (MQ=17)
                 aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   <  1:1798671/140‑1 (MQ=17)
                 aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAGGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   >  1:5138455/1‑140 (MQ=12)
                 aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCGGGCTCAGTCATTGCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACGGTTTCTTCGCCCTTTa   >  2:563555/1‑140 (MQ=11)
                 aCGCAAATTTAGGGAAGGTGAGAATAAGCAGAGAAATTCTTCTCGGCTGACTCAGAACTTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCCTTTCTTCGCCATTTa   <  2:2090632/140‑1 (MQ=11)
                  cGCAAATTTAGGGAAGGTGCGACTAAGCGGGGCAGTTCTTCTCGGCTGACTCAGTCATGTCATTTCTTCATGTTTGAGCCGGTTTGTTCTCCCGTAAATGGCTTGGATGAGCCTAGTTAGCCCGTTTCTTCGCCCTTTaa  >  2:1273270/1‑140 (MQ=11)
                                                                                                                                         |                    
TAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAA  >  NZ_CP025268/3652694‑3652851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAAGGCGTTATCC  >  NZ_CP025268/3652683‑3652861
                                                                                                                                                    |                              
GAAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAC                              <  SRR14920167.1814022/151‑1 (MQ=60)
 AAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCCGCCTATTTAGACC                             <  SRR14920167.5382273/151‑1 (MQ=60)
 AAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACC                             <  SRR14920167.761368/151‑1 (MQ=60)
 AAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACC                             <  SRR14920167.4441682/151‑1 (MQ=60)
 AAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACC                             <  SRR14920167.4311610/151‑1 (MQ=60)
   GATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGT                           >  SRR14920167.5454692/1‑151 (MQ=57)
   GATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGT                           >  SRR14920167.5349617/1‑151 (MQ=57)
   GATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGT                           >  SRR14920167.4343483/1‑151 (MQ=57)
      CTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTC                        >  SRR14920167.3986093/1‑151 (MQ=50)
      CTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATATTTAAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTC                        >  SRR14920167.3985831/1‑151 (MQ=48)
        ACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTT                      >  SRR14920167.3009383/1‑151 (MQ=46)
             ATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCA                 >  SRR14920167.154047/1‑151 (MQ=36)
             ATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCA                 >  SRR14920167.2451933/1‑151 (MQ=36)
             ATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCA                 >  SRR14920167.1467507/1‑151 (MQ=36)
             ATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTCAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCC                 >  SRR14920167.3122010/1‑151 (MQ=35)
              TATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCAT                <  SRR14920167.2330429/151‑1 (MQ=34)
                 AAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAGGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTA             >  SRR14920167.5150196/1‑151 (MQ=27)
                    TTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGG          >  SRR14920167.946124/1‑151 (MQ=21)
                    TTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGG          >  SRR14920167.946717/1‑151 (MQ=21)
                      TCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCG        <  SRR14920167.3996680/151‑1 (MQ=17)
                            ACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCC  <  SRR14920167.1802377/151‑1 (MQ=0)
                            ACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTATCC  <  SRR14920167.78209/151‑1 (MQ=0)
                                                                                                                                                    |                              
GAAGATCTACTTAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAAGGCGTTATCC  >  NZ_CP025268/3652683‑3652861

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑