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
A34 F60 I1 R1 17 86.3 2937582 99.1% 2911143 139.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8791.C94.9% 131.0 / 0.2 39coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (12/25);  total (13/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

TCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑C‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815740‑3816012
                                                                                                                                            |                                                                                                                                       
tCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt                                                                                                                                          <  1:769999/140‑1 (MQ=255)
           gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGc                                                                                                                             <  1:1102158/140‑1 (MQ=255)
                gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCagag                                                                                                                        <  1:1108053/140‑1 (MQ=255)
                   atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCca                                                                                                                     <  2:1103964/140‑1 (MQ=255)
                   atGGTTTCATGCCTTCGCTCCGTATCTTATTTTTCTATAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCca                                                                                                                     <  1:518802/140‑1 (MQ=255)
                        ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAg                                                                                                                <  2:1434513/140‑1 (MQ=255)
                         tcgtGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGa                                                                                                               >  2:936110/4‑140 (MQ=255)
                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGGCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:1004328/1‑140 (MQ=255)
                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:1197766/1‑140 (MQ=255)
                              ccTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGt                                                                                                          <  2:728124/140‑1 (MQ=255)
                                ttCGCTCCTCATCTTTCTTTTCTACGGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:580243/140‑1 (MQ=255)
                                ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:7297/140‑1 (MQ=255)
                                ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:1338522/140‑1 (MQ=255)
                                        tcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑C‑CACCTCGGGCCAGGGCGAACAAGGTGAGTAGCTCTTCAt                                                                                                >  1:710372/1‑140 (MQ=255)
                                              tACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGa                                                                                          >  2:747573/1‑140 (MQ=255)
                                                   ttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     >  1:1054443/1‑140 (MQ=255)
                                                     cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                   <  2:737879/140‑1 (MQ=255)
                                                             aaaaaaaaGGCGACTCATCAGTAGCCTTAAAGATCTGTTCGCCAGCGCAGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                           <  2:440971/140‑1 (MQ=255)
                                                                    aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:1004328/140‑1 (MQ=255)
                                                                    aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:163206/140‑1 (MQ=255)
                                                                     ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                   >  1:1347477/1‑140 (MQ=255)
                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:794497/140‑1 (MQ=255)
                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:319076/140‑1 (MQ=255)
                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:1347477/140‑1 (MQ=255)
                                                                         aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                               <  1:1233330/140‑1 (MQ=255)
                                                                                  tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTAAACGGCTAGCCATCGGCCGTCGCCTGCACTTCAatga                                                      >  1:613003/1‑140 (MQ=255)
                                                                                    gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                    >  2:790830/1‑140 (MQ=255)
                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:171846/1‑140 (MQ=255)
                                                                                        tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                                <  2:171846/140‑1 (MQ=255)
                                                                                        tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGACCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                                <  2:929911/140‑1 (MQ=255)
                                                                                             aTCAGTTTGCCAGCGCCACCTTATGCGTCGCCACAATGGTTTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                           <  2:613003/140‑1 (MQ=255)
                                                                                              tCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                          <  1:1242515/140‑1 (MQ=255)
                                                                                                  tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 <  2:320179/129‑1 (MQ=255)
                                                                                                  tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:320179/1‑129 (MQ=255)
                                                                                                    tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                    <  2:1197766/140‑1 (MQ=255)
                                                                                                        aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                <  2:328859/140‑1 (MQ=255)
                                                                                                             cgccTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                           <  2:1054443/140‑1 (MQ=255)
                                                                                                               ccTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTc                         >  2:1264793/1‑140 (MQ=255)
                                                                                                                       gTCGCTACAATGGATTCGATT‑CTC‑CCTCGCGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  1:434120/140‑1 (MQ=255)
                                                                                                                          gCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtctc              >  2:765489/1‑140 (MQ=255)
                                                                                                                                 tGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa       <  1:765489/140‑1 (MQ=255)
                                                                                                                                   gattcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     <  1:1264793/140‑1 (MQ=255)
                                                                                                                                      tcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTGGGTTATCCCTACGTTCATGTCTGTCTCTGCGGCAGAGTc  >  2:408322/1‑140 (MQ=255)
                                                                                                                                      tcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTGATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  2:603825/1‑140 (MQ=255)
                                                                                                                                      tcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGCTCATCACAACGATCTTGTCGGTCTCTGCGGCAGAGTc  >  1:520970/1‑140 (MQ=255)
                                                                                                                                      tcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCAGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:873223/1‑140 (MQ=255)
                                                                                                                                            |                                                                                                                                       
TCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑C‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815740‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A