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 F17 I0 R1 52 59.5 1410130 88.0% 1240914 215.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,424,240 G→T 34.8% L153F (TTG→TTT)  trkG → Rac prophage, potassium transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,424,2400GT34.8% 35.8 / 6.0 30L153F (TTG→TTT) trkGRac prophage, potassium transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (6/13);  new base T (9/2);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 2.09e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACT  >  NC_000913/1424016‑1424465
                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                   
ttttGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCa                                                                                                                                                                                                                                  <  2:106819/228‑1 (MQ=255)
          tGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTTTTGTT‑TTTCTATTTATTggga                                                                                                                                                                                                                        >  1:582224/1‑227 (MQ=255)
                             aTTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACACCAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGCGTTATTGTTCTGGCGG‑TTGGTGTA‑TTGCCA‑TTATTGGGGGTTGGTGGTGCTAAGCtttt                                                                                                                                                                                                    >  2:100503/1‑227 (MQ=255)
                               tCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTTGCC‑TTTTTGGGGTTTGTTGGTGCTAAGtttttt                                                                                                                                                                                                   >  2:236322/1‑225 (MQ=255)
                               tCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCGGGCGG‑TTGC‑GTATTTGTAT‑TTATTGTGGATTTGGGGTGCAAAGCgttctt                                                                                                                                                                                                  >  2:97745/1‑225 (MQ=255)
                                    ttATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATCACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTTTTTTTCTGGCGG‑TTGCTTCA‑TTTTTC‑TTATTTGGGTTTGgtggtgttattctttataaggta                                                                                                                                                                                             >  1:467018/1‑211 (MQ=255)
                                    ttATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTTTAGTTGGTTTAGGGGTTATTGTTCTGGCGGTTTTGTGTT‑TTTCCT‑TTTTTGGGT‑TTggtggttggcaagtttttaagtcg                                                                                                                                                                                             >  1:447593/1‑210 (MQ=255)
                                    ttATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TGGTTGTA‑TTGCCC‑TTATTTGGGATTGTTGGGTCGAAGCTTTTtcagtct                                                                                                                                                                                             >  2:632212/1‑227 (MQ=255)
                                               cctaggaCTTAATTTAACGTTCATTGATTCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCggg                                                                                                                                                                                  <  2:582224/222‑1 (MQ=255)
                                                       ttAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTa                                                                                                                                                                          <  2:447593/228‑1 (MQ=255)
                                                                cGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTTCTGTA‑TTTTAC‑TTTTTTGGTATTGGTGGTGCAATGCTGTTTTATTCTGAAAAGACCGGGGCGTTTAAGGATGAc                                                                                                                                                                  >  1:38577/1‑227 (MQ=255)
                                                                    cATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTTTCA‑TTATTGGGGGATGGTTGGTCAAAGCTTTATTAGTCCGGAATGCCGGGGCCATTTAATGATGACAAac                                                                                                                                                              >  2:319631/1‑227 (MQ=255)
                                                                        tattttttttttGAAGGGGTTTCTGGAAAAACAACAACAGGAGCAACTTTAATTGATGAGGTTAGTTTATTGCCTGGGGCATGTTTGTTTTTTCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCGGGCGG‑TTGATGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAactcact                                                                                                                                                         <  1:100503/219‑1 (MQ=255)
                                                                                       ggggttttttgttaaacaacaacAGGAGTAAGTGTAATTGATTATTTTATTTTATTGCCTTGTGCATATTTTTACTTTCGGTCCCAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCGGTA‑TTGCCA‑TTATTGGGTATTGGGGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGAt                                                                                                                                          <  1:236322/214‑1 (MQ=255)
                                                                                           tttCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTTcc                                                                                                                                                                                                                                   >  1:208118/1‑136 (MQ=255)
                                                                                            ttCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCa                                                                                                                                                                                                                                  <  2:208118/136‑1 (MQ=255)
                                                                                                    tAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTTGTGTA‑TTTCCA‑TTTTTTGGTGTTGGTGGTGGAAAAGTTTTTCTTGTAGAAATGCCCGGGCGCTTTTAGGGTGTAAAAACCCCTCCCCCCCCGGcccgaacggccagggaaa                                                                                                                             >  1:391418/1‑212 (MQ=255)
                                                                                                                     aCTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCt                                                                                                           <  2:38577/228‑1 (MQ=255)
                                                                                                                         ttaTTGATGTTTTTATTTTATTTCCTGGGGCATTTTTTTATTTTCGGTCAAAGTTAAATTTTATAGGTGGTTTAGGATTTATTGTTCTGGGGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTttat                                                                                                       <  1:38644/226‑1 (MQ=255)
                                                                                                                            ttGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTttatt                                                                                                      <  2:484830/226‑1 (MQ=255)
                                                                                                                               atgatgTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGGATTGGTGGTGCAAAGCTTTTTTAGTCAGAAAAGGCCGGGCCATTTAAGGATGACAAAACCACTTCCCGCCCTGCCGATACGTCACGGACAACTGGGGAAAACtatttccgtctctttt                                                                                                  >  2:590539/1‑213 (MQ=255)
                                                                                                                                 gatgTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTttatta                                                                                                     <  2:95131/222‑1 (MQ=255)
                                                                                                                                            aTTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGt                                                                                    <  2:94947/228‑1 (MQ=255)
                                                                                                                                             gatatgtgtataatagtcagcTATTGGTCAAAGTTAAATTTTATAGGGGGTTTAGGATTTATTGTTCTGGCGG‑TTGCTGTA‑TGGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGt                                                                                    <  2:621209/207‑1 (MQ=255)
                                                                                                                                                               tACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTTCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCCGTCAGAAATGCCGGGGCCATTTTAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGGA‑ACTTTGGATAAATTATTTTTTATTAGGGATTGCTTTGAATGGCTGTTATAGACttttcgga                                                                 >  2:153648/1‑222 (MQ=255)
                                                                                                                                                                    tCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGGTTTATTAGTTAGAAATGCCGGGGCCATTTAAGGATGGCAAACTCACTCCCCCCCTGGCCGCTACGCCACGGAC‑ACTGTGGGGAACTTATTCTTTATTTTGTGTTGGTTGTATTGTCTGTTATTTACTTTCAGGGATgtc                                                            >  1:494607/1‑226 (MQ=255)
                                                                                                                                                                            aGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGTTGTA‑TTGTCC‑TTATTTGGTATTTGTGTTTGCAAGCTTTATTCGTCAGAAATGCCCGTGACATTTTATGAGTATAAACTCCATCCCCCCCTCGCCCATACGCCCCCGGA‑ACTGCGGATTAATTACTCTTTTTTTTGTTTTTCTTTTATTGTCTGTTTTAGAcccgtttctttttcccaactaa                                                    >  1:621209/1‑207 (MQ=255)
                                                                                                                                                                                          ggttgtTTTGGTGTTTTTTTTCTTGCTG‑TTGCTGTA‑TTTCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAATCTACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCAc                                      <  1:153648/228‑1 (MQ=255)
                                                                                                                                                                                                                           tttA‑TTTCCA‑TTATTGGGTTTTGGTGGTGCAAAGCTTTATCAGTCAGAAAGGCCGGGGCAATTTAAGGATGAAAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTtctc      <  1:537546/226‑1 (MQ=255)
                                                                                                                                                                                                                                 tGCCA‑TTATTGGGTTTTGGGGGTGCAAAGCTGTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGTAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACt  <  2:467018/227‑1 (MQ=255)
                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                   
TTTTGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGG‑TTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGAC‑ACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACT  >  NC_000913/1424016‑1424465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A