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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,457,801 A→G Y102C (TAC→TGC)  paaF → 2,3‑dehydroadipyl‑CoA hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,457,8010AG100.0% 64.8 / NA 19Y102C (TAC→TGC) paaF2,3‑dehydroadipyl‑CoA hydratase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (6/13);  total (6/13)

CCGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTACGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTA  >  NC_000913/1457675‑1457928
                                                                                                                              |                                                                                                                               
ccGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGTTTGGGGc                                                                                                                     <  2:548795/139‑1 (MQ=255)
        gCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCg                                                                                                             <  2:657989/139‑1 (MQ=255)
             tctcAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTg                                                                                                        >  2:127/1‑139 (MQ=255)
                          gCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCg                                                                                           <  1:388827/139‑1 (MQ=255)
                                              cACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGgagag                                                                       <  2:443637/139‑1 (MQ=255)
                                                               gTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGtt                                                      >  1:470473/1‑139 (MQ=255)
                                                                tCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     >  1:133938/1‑91 (MQ=255)
                                                                tCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCa                                                                                                     <  2:133938/91‑1 (MQ=255)
                                                                       cTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGc                                                                                                                     <  1:302406/68‑1 (MQ=255)
                                                                       cTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGc                                                                                                                     >  2:302406/1‑68 (MQ=255)
                                                                        tATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAAt                                             <  1:127/139‑1 (MQ=255)
                                                                        tATGGGCGCGAGTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGTGAACGCGCGTTTTGGGTTGCCGGAAAt                                             <  1:543127/139‑1 (MQ=255)
                                                                                                   aaCCACTTATCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAgg                  <  1:688314/139‑1 (MQ=255)
                                                                                                           aTCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGga                                                                          <  2:131011/75‑1 (MQ=255)
                                                                                                           aTCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGga                                                                          >  1:131011/1‑75 (MQ=255)
                                                                                                            tCGCAGCCGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCa         <  1:216200/139‑1 (MQ=255)
                                                                                                                  ccGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGtggtgg                                                                                  <  2:771063/60‑1 (MQ=255)
                                                                                                                  ccGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGtggtgg                                                                                  >  1:771063/1‑60 (MQ=255)
                                                                                                                   cGTCAATGGTTGCGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTa  <  2:470473/139‑1 (MQ=255)
                                                                                                                              |                                                                                                                               
CCGCTGGGGCCGATCTCAACGAAATGGCAGAAAAAGATCTCGCGGCCACCTTAAACGATACACGTCCGCAGCTATGGGCGCGATTGCAGGCCTTTAATAAACCACTTATCGCAGCCGTCAATGGTTACGCGCTTGGGGCGGGTTGCGAACTGGCATTGTTGTGCGATGTGGTGGTTGCCGGAGAGAACGCGCGTTTTGGGTTGCCGGAAATCACTCTCGGCATCATGCCTGGCGCAGGCGGAACGCAACGTTTA  >  NC_000913/1457675‑1457928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A