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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 236,541 C→T R159* (CGA→TGA)  dnaQ → DNA polymerase III epsilon subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913236,5410CT96.4% 183.0 / ‑3.0 56R159* (CGA→TGA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base C (0/2);  new base T (29/25);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CACCGATAGCCTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAACGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATGGAAG  >  NC_000913/236447‑236637
                                                                                              |                                                                                                
cACCGATAGCCTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAaatgaacg                                                                                             <  2:199669/100‑1 (MQ=255)
    gATAGCCTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGc                                                                                         >  1:654523/1‑100 (MQ=255)
        gCCTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACgg                                                                                     >  1:202646/1‑100 (MQ=255)
         ccTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCATCAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACgg                                                                                     <  2:167566/99‑1 (MQ=255)
         ccTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACggg                                                                                    >  1:133171/1‑100 (MQ=255)
            tGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCa                                                                                 <  1:128150/100‑1 (MQ=255)
             gCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCAt                                                                                >  1:195937/1‑100 (MQ=255)
                 tGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACt                                                                            <  1:257902/100‑1 (MQ=255)
                       ggAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAACTAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGc                                                                      >  2:1008406/1‑100 (MQ=255)
                       ggAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGc                                                                      <  2:153398/100‑1 (MQ=255)
                       ggAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGc                                                                      <  1:517890/100‑1 (MQ=255)
                       ggAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGc                                                                      >  2:894488/1‑100 (MQ=255)
                            aTGTTTCCCGCTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAACGAGCGCTGCACGGGGCATTACTCGATGCCCAGa                                                                 <  2:1031356/100‑1 (MQ=255)
                             tGTTTCCCGATAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGAt                                                                >  1:300815/1‑100 (MQ=255)
                                ttCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCt                                                             >  1:797515/1‑100 (MQ=255)
                                 tCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCtt                                                            >  2:84779/1‑100 (MQ=255)
                                   ccGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGc                                                          >  1:917552/1‑100 (MQ=255)
                                    cGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCg                                                         >  2:607601/1‑100 (MQ=255)
                                    cGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCg                                                         <  2:990479/100‑1 (MQ=255)
                                     ggTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCgg                                                        >  1:1160189/1‑100 (MQ=255)
                                        aaGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAg                                                     <  2:821232/100‑1 (MQ=255)
                                         ngcgcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGt                                                    >  1:844378/2‑100 (MQ=255)
                                          gcgcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGtt                                                   <  1:139596/100‑1 (MQ=255)
                                          gcgcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGtt                                                   >  2:52665/1‑100 (MQ=255)
                                          gcgcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGtt                                                   >  2:1382457/1‑100 (MQ=255)
                                            gcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTa                                                 <  2:590776/100‑1 (MQ=255)
                                            gcAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTa                                                 <  1:1430360/100‑1 (MQ=255)
                                              aaCAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATc                                               <  1:975167/100‑1 (MQ=255)
                                                 aGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTgg                                            <  2:930541/100‑1 (MQ=255)
                                                  gCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGc                                           <  1:728126/100‑1 (MQ=255)
                                                   ccTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCg                                          >  1:151755/1‑100 (MQ=255)
                                                       gATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGa                                      >  1:676711/1‑100 (MQ=255)
                                                         tGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGAcc                                    <  2:1097580/100‑1 (MQ=255)
                                                           cGTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCgg                                  <  1:1382467/100‑1 (MQ=255)
                                                            gTTATGTGCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCggt                                 <  2:202645/100‑1 (MQ=255)
                                                               aTGTGCTCGCTACGAAATAGATAACAGTAAACGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCggtggt                              <  2:1047179/100‑1 (MQ=255)
                                                                   gCTCGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCaaa                          >  2:541117/1‑100 (MQ=255)
                                                                      cGCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGt                       >  2:271915/1‑100 (MQ=255)
                                                                       gCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTc                      >  1:866434/1‑100 (MQ=255)
                                                                       gCTACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTc                      <  1:607604/100‑1 (MQ=255)
                                                                         tACGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGa                    >  2:814316/1‑100 (MQ=255)
                                                                          aCGAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGAt                   <  1:994289/100‑1 (MQ=255)
                                                                            gAAATAGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATgg                 <  1:424238/100‑1 (MQ=255)
                                                                             aaataaatAACAGTAAATGAACGCTGCACGGGGCCATACGCGAGGCCCAGATCCTTGCGGAAGTTGATCTGGCGATGACCGGTGGTCAAACGTCGATgtc                <  2:147706/100‑3 (MQ=255)
                                                                                 aGATAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCtttt            <  2:1353839/100‑1 (MQ=255)
                                                                                    tAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCg         <  1:84779/100‑1 (MQ=255)
                                                                                    tAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCg         <  1:865478/100‑1 (MQ=255)
                                                                                    tAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCg         <  1:866049/100‑1 (MQ=255)
                                                                                    tAACAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCg         >  1:256157/1‑100 (MQ=255)
                                                                                     aaCAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCg         >  2:1243969/1‑99 (MQ=255)
                                                                                       cAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATg      >  2:1414412/1‑100 (MQ=255)
                                                                                       cAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATg      >  1:1389093/1‑100 (MQ=255)
                                                                                       cAGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATg      >  2:1192371/1‑100 (MQ=255)
                                                                                        aGTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATgg     >  2:528891/1‑100 (MQ=255)
                                                                                         gTAAATGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATGGa    <  1:1414422/100‑1 (MQ=255)
                                                                                           aaaTGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATGGAAg  >  2:395235/1‑100 (MQ=255)
                                                                                           aaaTGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATGGAAg  >  2:1288509/1‑100 (MQ=255)
                                                                                              |                                                                                                
CACCGATAGCCTTGCGGTGGCGAGGAAAATGTTTCCCGGTAAGCGCAACAGCCTCGATGCGTTATGTGCTCGCTACGAAATAGATAACAGTAAACGAACGCTGCACGGGGCATTACTCGATGCCCAGATCCTTGCGGAAGTTTATCTGGCGATGACCGGTGGTCAAACGTCGATGGCTTTTGCGATGGAAG  >  NC_000913/236447‑236637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A