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 F107 I1 R1 11 42.4 1464626 94.8% 1388465 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,277,819 G→T G118* (GGA→TGA)  soxR → redox‑sensitive transcriptional activator of soxS, autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,277,8190GT87.8% 101.5 / ‑5.4 42G118* (GGA→TGA) soxRredox‑sensitive transcriptional activator of soxS, autorepressor
Reads supporting (aligned to +/- strand):  ref base G (1/4);  new base T (20/16);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGT  >  NC_000913/4277680‑4277958
                                                                                                                                           |                                                                                                                                           
gACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGAt                                                                                                                                          >  2:294762/1‑143 (MQ=255)
    aTTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAGGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCGGCGTGACGAACCGGACTGACGTAt                                                                                                                                      >  2:718197/1‑143 (MQ=255)
        gTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGt                                                                                                                                  >  2:486253/1‑143 (MQ=255)
           aaGCGTTTAGCGTGTTGTTTGAAGGGTATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTtgt                                                                                                                               <  1:231224/143‑1 (MQ=255)
             gCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTgg                                                                                                                             <  1:411503/143‑1 (MQ=255)
                 ttGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGCCGCTGCGTGACGAACTGGACTGACGTCTTGGTGGTGGCTGc                                                                                                                         >  1:513258/1‑143 (MQ=255)
                     cttgtTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATGCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCttt                                                                                                                     <  2:362840/141‑1 (MQ=255)
                           ggccGAAGGGCATACGGTGGGTGGGAAAGAGTGTAAACAGCTGTCGGCCCAACGGCGGGAAGAGTTGGATCGGCGCATTCATACCTTGGTGGCGCGGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCa                                                                                                               <  2:283699/141‑1 (MQ=255)
                              cGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTg                                                                                                            >  1:313731/1‑143 (MQ=255)
                                    gCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCGTACCTTAGTGGCGCTGCGTGAGGACCTGGACTGATGTCTTGGTTGTGGCTGGCTTTCGCGCGGTGATTggc                                                                                                      >  2:107473/1‑141 (MQ=255)
                                       tACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCCTCCCTTAGTGGCGCTGCGTGACGAACTTTACGTATGGATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGt                                                                                                   >  1:199418/1‑143 (MQ=255)
                                        aCGTTAGGTGCGAGAGCGGCGAAACAGCTTTCGTCCCAGTGGCGAGAAGAGGTGGATCGGCGCATTCATGCCTTAGTGGGGCTGCGTGACGAACTGGACTGGTGTGTGGGTGGTGGCTGCCTTGCGCGCAGTGATTGCCCGtt                                                                                                  <  2:72420/143‑1 (MQ=255)
                                           ttAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCAGTCATACCTTAGTGGCGCTGCGTGACGAACTGGACAGATGTAATGGATGTGGCAGCCATTAGCGCAGTGACTGCCCGTTGCg                                                                                               >  2:552561/1‑143 (MQ=255)
                                             aaGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCttt                                                                                                                     <  1:187559/119‑1 (MQ=255)
                                             aaGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCttt                                                                                                                     >  2:187559/1‑119 (MQ=255)
                                                tGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAGGTGGATTCATGTTGTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAAca                                                                                          >  1:531151/1‑142 (MQ=255)
                                                    aaaGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGATTTCCGCGCTGCGATTGCCCGTTGCGTAACCCggg                                                                                      >  1:132669/1‑143 (MQ=255)
                                                               aCAGCTTTCGTCCCAATGGCGAGAAGAGTTGTATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAg                                                                           <  1:662626/143‑1 (MQ=255)
                                                               aCAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGCTTGCCCGTTGCGTAACCCGGGCGACCGCTTAg                                                                           >  1:221570/1‑143 (MQ=255)
                                                               aCAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAg                                                                           >  1:630943/1‑143 (MQ=255)
                                                                cAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGGCCGTTGCGTAACCCGGGCGGCCGCTTAgg                                                                          >  1:491390/1‑143 (MQ=255)
                                                                     ttCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGGACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGATCGCTTCTGagaag                                                                     >  2:98912/1‑143 (MQ=255)
                                                                     ttCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGagaag                                                                     <  1:499626/143‑1 (MQ=255)
                                                                     ttCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGagaag                                                                     <  1:486253/143‑1 (MQ=255)
                                                                       cgccccAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAgaagaa                                                                   <  1:272606/140‑1 (MQ=255)
                                                                            cAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTCGTGGCGCTGCGTGACCAACTGGACTGACGGCTTGCTTGTGGCTGCCTTTCGCCCCCTGATTGCGCGCTCCGTAACCCGGCCCACCCCCTCGGAGAAGAAGCTAc                                                              >  2:568168/1‑143 (MQ=255)
                                                                            cAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTAc                                                              <  1:192829/143‑1 (MQ=255)
                                                                              aTGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCg                                                            <  1:547002/143‑1 (MQ=255)
                                                                                          gTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGc                                                <  2:313731/143‑1 (MQ=255)
                                                                                            tGGATCGGCGCATTCCTACCTTCGTGACGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTg                                              <  1:129853/143‑1 (MQ=255)
                                                                                             gcgtCGGCGCATGCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTgg                                             <  2:405763/140‑1 (MQ=255)
                                                                                                tCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTCCCCGCGCACGCTTGCCGCAAg                                          >  2:652287/1‑143 (MQ=255)
                                                                                                tCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACGGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGAGACAGGGGCGACCGACTCGGAGAAGAAGGTACCGGCGCCAGCGTGCTGGAAg                                          >  2:475975/1‑143 (MQ=255)
                                                                                                      cATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAAc                                    >  1:98688/1‑143 (MQ=255)
                                                                                                      cATTCATACCTTAGGGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGAGTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAAc                                    <  1:214441/143‑1 (MQ=255)
                                                                                                        ttCATACCTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACaa                                  >  1:258744/1‑143 (MQ=255)
                                                                                                               cTTAGTGGCGCTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGCCGAAGGTCCCGGCGCCGGCTTGCTGCGAGCTGAACACAAATata                           >  1:275168/1‑141 (MQ=255)
                                                                                                                    gtgcgcTGCGTGACGGGCGGGACGGATGGATGGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGcc                      <  2:88768/141‑1 (MQ=255)
                                                                                                                      gcgcTGCGTGACGAACTGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCcac                    >  1:446670/1‑143 (MQ=255)
                                                                                                                                      tGGACTGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGAGGGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAgttt    <  1:689504/143‑1 (MQ=255)
                                                                                                                                       ggACGGATGTATTGGTTGTGGCTGCCTTTGACGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAgtttg   <  2:458711/143‑1 (MQ=255)
                                                                                                                                        ggcGGATGTACTGGTTGTGGCTGCTTTTCGGGGAGTGATTGACCGTTGTGTAACGCGTCCGACTGGTTAGGAGAAGAAGGTGTAGGCGCACGCTTGCTGGAAGATGAATAAAACTAAAGCGCCACAAGGGCGCTTTAgtttgt  <  2:219493/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                           
GACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAAAGCGCCACAAGGGCGCTTTAGTTTGT  >  NC_000913/4277680‑4277958

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A