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 3,583,454 G→A intergenic (+36/‑29) yrhA → / → insA pseudogene, interrupted by IS1E/IS1 repressor TnpA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,583,4540GA100.0% 59.7 / NA 22intergenic (+36/‑29)yrhA/insApseudogene, interrupted by IS1E/IS1 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (12/10);  total (12/10)

TAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATC  >  NC_000913/3583337‑3583564
                                                                                                                     |                                                                                                              
taGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                           <  2:346794/139‑1 (MQ=255)
                ttCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                           >  1:280537/1‑139 (MQ=255)
                             aTCTACAAGAACGGTTAGTGATTGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCt                                                              >  1:410099/1‑139 (MQ=255)
                                  cAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTatgatg                                                                                                       <  2:814856/93‑1 (MQ=255)
                                  cAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTatgatg                                                                                                       >  1:814856/1‑93 (MQ=255)
                                   aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGt                                                                                  <  1:240289/113‑1 (MQ=255)
                                   aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGt                                                                                  >  2:240289/1‑113 (MQ=255)
                                          gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                                          >  2:52870/1‑114 (MQ=255)
                                          gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                                          <  1:52870/114‑1 (MQ=255)
                                          gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTc                                                 >  1:195764/1‑139 (MQ=255)
                                                   cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGa                                        <  2:165179/139‑1 (MQ=255)
                                                     gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATgg                                                                                                      >  1:717126/1‑75 (MQ=255)
                                                     gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATgg                                                                                                      <  2:717126/75‑1 (MQ=255)
                                                                 tttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTTAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                               <  1:770062/102‑1 (MQ=255)
                                                                 tttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTTAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                               >  2:770062/1‑102 (MQ=255)
                                                                               tATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTa                          <  2:25390/125‑1 (MQ=255)
                                                                               tATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTa                          >  1:25390/1‑125 (MQ=255)
                                                                                     aTTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGa      >  1:781670/1‑139 (MQ=18)
                                                                                       tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACa    >  2:194144/1‑139 (MQ=17)
                                                                                        aaaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                                            <  2:195581/82‑1 (MQ=17)
                                                                                        aaaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                                            >  1:195581/1‑82 (MQ=17)
                                                                                         aaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATc  <  2:280537/139‑1 (MQ=11)
                                                                                                                     |                                                                                                              
TAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATC  >  NC_000913/3583337‑3583564

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A