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
A17 F61 I0 R1 36 35.4 1352518 90.1% 1218618 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,196,196 T→C 32.6% intergenic (‑97/+136) thiC ← / ← rsd phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,196,1960TC32.6% 35.8 / 22.2 37intergenic (‑97/+136)thiC/rsdphosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand):  ref base T (16/8);  new base C (4/8);  total (20/17)
Fisher's exact test for biased strand distribution p-value = 8.15e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

GCCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCA  >  NC_000913/4196056‑4196327
                                                                                                                                            |                                                                                                                                   
gCCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTc                                                                                                                                   >  1:431000/1‑143 (MQ=255)
gCCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTc                                                                                                                                   <  2:126406/143‑1 (MQ=255)
            tgttCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATAGCCGCAGGGGCGATGCGATAGCAGATTAACGCATGCTCCCTTCGAAggaa                                                                                                                       >  2:602907/1‑141 (MQ=255)
                 gcggcgGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGc                                                                                                                  >  2:592121/1‑143 (MQ=255)
                   cgctggTCAGTTTTCTTGCAGCCATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGCGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCt                                                                                                                <  1:76873/139‑1 (MQ=255)
                    gttgtgcAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTATGGATCTTGTTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCTGTTGCGTGGTGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTg                                                                                                               <  2:108602/137‑1 (MQ=255)
                                        aCATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCCGGTATTAGCCTGATCAGGTTCCGCGGATCCCg                                                                                           >  2:96096/1‑143 (MQ=255)
                                           tAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAAt                                                                                        <  1:324242/143‑1 (MQ=255)
                                               tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTCACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCGGAATaacc                                                                                    >  2:533710/1‑141 (MQ=255)
                                                cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCACAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTAGCAGGTATTAGCGTGATCAGGTTCTGCGGATCCCGAAGAAACg                                                                                   >  2:131715/1‑143 (MQ=255)
                                                  ttgcAAAAAGTTAAGGGCGTGGCTGGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGt                                                                                 <  2:634586/140‑1 (MQ=255)
                                                      tgaaaGGTAAGGGCGTGGCGTGTCCGACGAGGGATGAAGCGAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATGAACTCTTGTTCCCTTCGCATGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAATCGGttcca                                                                             <  2:448568/141‑5 (MQ=255)
                                                      aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTGTCa                                                                             >  1:511918/1‑143 (MQ=255)
                                                          aGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCAGCCa                                                                         <  1:241168/143‑1 (MQ=255)
                                                             tAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCAGCCAGtt                                                                      >  1:40747/1‑143 (MQ=255)
                                                               aGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGCTCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa                                                                    <  1:496498/143‑1 (MQ=255)
                                                                ggtgtcggCTTGTCGGGCGACGGATGAATCAGGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTGGCTCCCTTCGCAGGTATTAGCCTGATGAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg                                                                   <  2:669702/137‑1 (MQ=255)
                                                                ggACCTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCAGCCAGTTAAg                                                                   <  1:592314/143‑1 (MQ=255)
                                                                 gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGAACCCCCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCAGCCAGTTAAgg                                                                  >  1:25310/1‑143 (MQ=255)
                                                                  aCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGAGGCGATGCGATAGCAGATTCACTCTTGTTCCCGTCGCAGGTATTAGACTGATCAGGTTCGGAGGGTCACGAAATAACGGAATCAGCCAGTTAAGGc                                                                 >  2:53276/1‑143 (MQ=255)
                                                                      ggCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCGCTc                                                             >  1:86714/1‑143 (MQ=255)
                                                                         ttGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGa                                                          >  1:651728/1‑143 (MQ=255)
                                                                               gacgacGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGCCAAGaa                                                    >  2:606269/1‑143 (MQ=255)
                                                                                   acgGAAGAATCAACTGACGAGTGCCGCAGGGGCGATGCGATAGCAGATGATCTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCGGCCAGTTAAGGCACTCCGACAAGAAATTa                                                <  2:590757/143‑1 (MQ=255)
                                                                                      gATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCGTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGcc                                             <  1:202917/143‑1 (MQ=255)
                                                                                        tGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCCGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGcccc                                           <  2:40859/143‑1 (MQ=255)
                                                                                         gAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATCAGCCTGAGCAGCTTCCGCGGGTCCCGACTAAACGGTCTCAGCCAGTTAAGGCACGCCGACAAGAAAAGAGCcgcg                                          >  2:429577/1‑143 (MQ=255)
                                                                                             cAAGCGACCATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaaa                                      <  1:375549/143‑1 (MQ=255)
                                                                                              aaGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCCCAGCCAGTTAAGGCACTCCGACAAGAAAATAGCCCCGCAAAt                                     >  2:513829/1‑143 (MQ=255)
                                                                                                gagcCGATCGGCGCCGGCGCGATGCGATAGCAGATGAGCTCTTGCGCTCTTCGCAGGTATTAGCCTGATCACGTTCCGCGCATCCTGTATAAACGGTCGCAGCCAGTTAAGGCACTCAGACAAGAAATTAGCCCCGCAAATgg                                   <  2:101414/143‑1 (MQ=255)
                                                                                                 agaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATggg                                  >  1:133153/1‑143 (MQ=255)
                                                                                                 agaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATggg                                  >  1:157944/1‑143 (MQ=255)
                                                                                                   aCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGc                                >  1:288773/1‑143 (MQ=255)
                                                                                                          cccctgcggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAAt                         >  1:206756/8‑143 (MQ=255)
                                                                                                            gcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTATCAGCCAGTTAAGGCACTCCGCCAAGAAATTAGCGCCGCAAACGGGGCGTTGAATGt                       >  2:213593/1‑143 (MQ=255)
                                                                                                                           caGCATATTAACTCTTGGTCCCTTCGCAGGTATTAGCCTGATCAGGGTCCGCGGATCGCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAAc        <  2:321761/142‑1 (MQ=255)
                                                                                                                                 aTTAACTCCTGTTACCTTCGTAGGTATGAGCCTGATCAGGTTCCGCGGACCCCGAATAAACGGTCTCAGCCAGTTAAGGCACGCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa  <  2:599829/143‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                   
GCCCGGGCGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCA  >  NC_000913/4196056‑4196327

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