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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 836,353 G→T 22.0% P357P (CCG→CCT)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,3530GT22.0% 144.9 / 22.7 59P357P (CCG→CCT) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base G (25/21);  new base T (7/6);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGCCAGACG  >  minE/836286‑836420
                                                                   |                                                                   
tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCct                                                                  >  1:2348671/1‑71 (MQ=255)
tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCct                                                                  <  1:1179151/71‑1 (MQ=255)
  gaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCctct                                                                >  1:1978771/1‑71 (MQ=255)
       gaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac                                                           >  1:1016794/1‑69 (MQ=255)
       gaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac                                                           >  1:2646398/1‑69 (MQ=255)
        aaaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGtcac                                                           <  1:351759/70‑3 (MQ=255)
        aaaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc                                                          <  1:1189360/71‑1 (MQ=255)
         aaCTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTcc                                                          >  1:2183290/1‑70 (MQ=255)
         aaCTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCg                                                         <  1:468770/71‑1 (MQ=255)
         aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTTCGTTCCTCCGCTGTCAcc                                                          >  1:1117825/1‑70 (MQ=255)
         aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc                                                          >  1:2949734/1‑70 (MQ=255)
         aaCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCAcc                                                          >  1:193198/1‑70 (MQ=255)
           cTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGAt                                                       >  1:1096156/1‑71 (MQ=255)
           cTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGAt                                                       >  1:2563832/1‑71 (MQ=255)
              gctctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCa                                                    <  1:1037688/68‑1 (MQ=255)
              gcgcTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCa                                                    <  1:938035/71‑1 (MQ=255)
                 ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTc                                                 <  1:2020396/71‑1 (MQ=255)
                  taccgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTcc                                                >  1:2225747/3‑70 (MQ=255)
                    ccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGAtt                                                      >  1:3817749/1‑63 (MQ=255)
                          cATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcagca                                          <  1:2173391/69‑1 (MQ=255)
                             ccGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc                                     >  1:3561121/1‑71 (MQ=255)
                             ccGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc                                     >  1:2260819/1‑71 (MQ=255)
                              cGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgcg                                    >  1:1220806/1‑71 (MQ=255)
                              cGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc                                     <  1:1796500/70‑1 (MQ=255)
                                 aaTATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGt                                                  >  1:2036560/1‑54 (MQ=255)
                                 aaTATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGt                                                  >  1:3003653/1‑54 (MQ=255)
                                 aaTATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGt                                                  >  1:821570/1‑54 (MQ=255)
                                 aaTACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTCCTACGCAGATGCgggc                                 <  1:1275251/71‑2 (MQ=255)
                                 aaTACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTCCTACGCAGATGCggg                                  <  1:3741691/70‑1 (MQ=255)
                                 aaTACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTCCTACGCAGATGCggg                                  <  1:3119297/70‑1 (MQ=255)
                                  atatCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGt                                 >  1:2564366/1‑70 (MQ=255)
                                     tCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc                                     <  1:3129493/63‑1 (MQ=255)
                                      cGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTg                                               <  1:247632/52‑1 (MQ=255)
                                       gCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTg                           >  1:1712031/1‑71 (MQ=255)
                                           acTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcagca                                          <  1:146365/52‑1 (MQ=255)
                                            cTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTcc                                                <  1:846643/45‑2 (MQ=255)
                                            cTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCa                                                    >  1:234595/1‑41 (MQ=255)
                                             tGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAg                      >  1:964562/1‑70 (MQ=255)
                                               ccGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGc                     <  1:631065/69‑1 (MQ=255)
                                               ccGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCa                    <  1:3462616/70‑1 (MQ=255)
                                                 gATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTgg                          <  1:1928373/62‑1 (MQ=255)
                                                 gATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACg                 <  1:579703/71‑1 (MQ=255)
                                                  aTGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTa                       >  1:2971127/1‑64 (MQ=255)
                                                  aTGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTa                       >  1:1195306/1‑64 (MQ=255)
                                                  aTGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTa                       >  1:3748732/1‑64 (MQ=255)
                                                  aTGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTa                       >  1:2695018/1‑64 (MQ=255)
                                                  aTGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAAc                  >  1:2731176/1‑69 (MQ=255)
                                                    ggTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcagca                                          >  1:3379391/1‑43 (MQ=255)
                                                    ggTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcagca                                          >  1:3326930/1‑43 (MQ=255)
                                                        tGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCt          >  1:1183955/1‑71 (MQ=255)
                                                         ggTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCaa                   <  1:2740904/61‑1 (MQ=255)
                                                         ggTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCaa                   <  1:2762203/61‑1 (MQ=255)
                                                          gTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc                                     <  1:3129222/42‑1 (MQ=255)
                                                          gTACGTGCCGCCTCTGTCTCCGATTCAGTCTGAAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGc        <  1:814513/71‑1 (MQ=255)
                                                           tACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGcc       <  1:3198261/71‑1 (MQ=255)
                                                            aCGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGc        >  1:1038961/1‑69 (MQ=255)
                                                             cGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGc                     <  1:1150529/55‑1 (MQ=255)
                                                             cGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGc        >  1:3051842/1‑68 (MQ=255)
                                                               tGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGCCAGAc   <  1:2780234/71‑1 (MQ=255)
                                                                 ccgccTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGCCAGACg  <  1:1455609/70‑1 (MQ=255)
                                                                 ccgccTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGCCAGACg  <  1:1021084/70‑1 (MQ=255)
                                                                   |                                                                   
TGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGGTGAGCTGGGTAGCAACGGCATTCTGCCAGACG  >  minE/836286‑836420

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A