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 1,486,279 T→C 35.1% T345A (ACA→GCA)  nuoN ← NADH:ubiquinone oxidoreductase, membrane subunit N

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,486,2790TC35.1% 73.5 / 72.2 77T345A (ACA→GCA) nuoNNADH:ubiquinone oxidoreductase, membrane subunit N
Reads supporting (aligned to +/- strand):  ref base T (34/16);  new base C (19/8);  total (53/24)
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

CGCGCAGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCAGAGA  >  minE/1486210‑1486348
                                                                     |                                                                     
cgcgCAGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTc                                                                      >  1:2423008/1‑71 (MQ=255)
  cgcAGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTg                                                                    >  1:1512444/1‑71 (MQ=255)
    cAGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGa                                                                  <  1:994869/71‑1 (MQ=255)
       gtagtagtaGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGacac                                                               >  1:581129/1‑71 (MQ=255)
         agtagtagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACacc                                                              >  1:1486131/1‑70 (MQ=255)
          gtagtagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACaccga                                                            <  1:788863/71‑1 (MQ=255)
              tagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGc                                                        <  1:2717620/71‑1 (MQ=255)
              tagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGc                                                        <  1:1635841/71‑1 (MQ=255)
              tagAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGc                                                        >  1:3605331/1‑71 (MQ=255)
                gagGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGc                                                        >  1:3459974/1‑69 (MQ=255)
                gagGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGc                                                        >  1:2080269/1‑69 (MQ=255)
                  ggCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACaccgacc                                                          >  1:3917189/1‑65 (MQ=255)
                  ggCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAg                                                     >  1:1295455/1‑70 (MQ=255)
                    ccGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCAc                                                  <  1:29051/71‑1 (MQ=255)
                     cGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACg                                                 >  1:2382449/1‑71 (MQ=255)
                      gATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACg                                                 >  1:2601615/1‑70 (MQ=255)
                      gATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGt                                                <  1:1430735/71‑1 (MQ=255)
                        ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGaca                                                                >  1:1929043/1‑53 (MQ=255)
                        ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACg                                                 >  1:2762620/1‑68 (MQ=255)
                        ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                              <  1:494/71‑1 (MQ=255)
                        ttGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACC‑CCAGCACGTa                                               >  1:3475749/1‑69 (MQ=255)
                          gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGa                                                                  >  1:769753/1‑49 (MQ=255)
                          gCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGa                                             <  1:596873/70‑1 (MQ=255)
                            cGAACCGACAACCACGGCACCCACCAGCGACCACAAGTGTGCCTGGACaccg                                                             >  1:487880/1‑52 (MQ=255)
                            cGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCa                                                      <  1:1379347/59‑1 (MQ=255)
                            cGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACt                                          <  1:3053397/71‑1 (MQ=255)
                            cGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACt                                          <  1:3270816/71‑1 (MQ=255)
                             gAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACtt                                         <  1:3301133/71‑1 (MQ=255)
                              aaCCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTa                                        >  1:2438121/1‑71 (MQ=255)
                               aCCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTAc                                       >  1:47768/1‑71 (MQ=255)
                               aCCGACAACCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGaa                                            >  1:3242618/1‑66 (MQ=255)
                                   aCAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                    >  1:1980338/1‑70 (MQ=255)
                                   aCAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGAt                                   <  1:1637717/71‑1 (MQ=255)
                                    cAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATa                                  <  1:1570997/71‑1 (MQ=255)
                                     aaCCACGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATa                                  >  1:1546221/1‑70 (MQ=255)
                                      aCCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATa                                  >  1:3707157/1‑69 (MQ=255)
                                       ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACtt                                         <  1:3414598/61‑1 (MQ=255)
                                       ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                               >  1:3562819/1‑71 (MQ=255)
                                       ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                               >  1:1832736/1‑71 (MQ=255)
                                       ccACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAg                               >  1:112804/1‑71 (MQ=255)
                                        cACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGt                                                >  1:1472356/1‑53 (MQ=255)
                                         aCGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                             >  1:973028/1‑71 (MQ=255)
                                          cGGCACCCACCAGCCACCACAAGTGTGTCTGGACaccg                                                             >  1:2926712/1‑38 (MQ=255)
                                          cGGCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                             >  1:2182592/1‑70 (MQ=255)
                                           ggCACCCACCAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGcc                             >  1:2121258/1‑69 (MQ=255)
                                              acccaccAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAg                                              <  1:1386745/49‑1 (MQ=255)
                                              acccaccAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCg                        >  1:2748009/1‑71 (MQ=255)
                                              acccaccAGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCAAGCg                        >  1:1608993/1‑71 (MQ=255)
                                               cccaccAGCCAACACAAGTGTGCCTGGACACCGACCGCCAGCACGTAg                                              <  1:1968030/48‑1 (MQ=39)
                                                  accaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCagg                                                 >  1:2612877/1‑40 (MQ=255)
                                                  accaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTAcc                                      >  1:1860001/1‑53 (MQ=255)
                                                  accaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                    >  1:1563459/1‑55 (MQ=255)
                                                   ccaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATc                   >  1:10049/1‑71 (MQ=255)
                                                   ccaGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATc                   >  1:3862142/1‑71 (MQ=255)
                                                   ccaGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATc                   >  1:231862/1‑71 (MQ=255)
                                                    caGCCACCACAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCg                  >  1:725993/1‑71 (MQ=255)
                                                     aGCCACCACAAGTGTGCCTGGACACCGCCCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCgg                 >  1:1137682/1‑71 (MQ=255)
                                                      gCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATc                   >  1:581616/1‑68 (MQ=255)
                                                       ccaccaCAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGa               >  1:1996812/1‑71 (MQ=255)
                                                         accacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaa                                 <  1:1951040/51‑1 (MQ=255)
                                                         accacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATaa                                 <  1:383768/51‑1 (MQ=255)
                                                         accacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATa             >  1:131530/1‑71 (MQ=255)
                                                         accacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATa             >  1:2799817/1‑71 (MQ=255)
                                                          ccacAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCa                     <  1:2930335/62‑1 (MQ=255)
                                                          ccacAAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCa                           >  1:882889/1‑56 (MQ=255)
                                                           cacaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATAcc           >  1:1146936/1‑71 (MQ=255)
                                                           cacaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTc                      <  1:387705/60‑1 (MQ=255)
                                                           cacaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATAcc           >  1:2048537/1‑71 (MQ=255)
                                                           cacaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATAcc           >  1:459118/1‑71 (MQ=255)
                                                            acaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATc                   >  1:1632834/1‑62 (MQ=255)
                                                            acaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCg          <  1:1341291/71‑1 (MQ=255)
                                                            acaAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCg          >  1:395825/1‑71 (MQ=255)
                                                            acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTAc                                       >  1:3409457/1‑42 (MQ=255)
                                                            acaAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTAc                                       >  1:1604995/1‑42 (MQ=255)
                                                             caAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCgg         <  1:1417201/71‑1 (MQ=255)
                                                             caAGTGTGCCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATAGGGATACCgg         >  1:1521311/1‑71 (MQ=255)
                                                              aaGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTAcc                                      <  1:3917010/41‑1 (MQ=255)
                                                                gtgtgtCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                    >  1:1528534/1‑41 (MQ=255)
                                                                gtgtgtCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                    >  1:1461900/1‑41 (MQ=255)
                                                                gtgtgtCTGGACACCGACCGCCAGCACGTAGAACTTACCGa                                    >  1:3597435/1‑41 (MQ=255)
                                                                gtgtgcCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCa      <  1:3398424/71‑1 (MQ=255)
                                                                gtgtgcCTAGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGc        >  1:2063785/1‑69 (MQ=255)
                                                                  gtgtCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCa      >  1:2511837/1‑69 (MQ=255)
                                                                  gtgtCTGGACACCGAACGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCa      >  1:2143086/1‑69 (MQ=255)
                                                                  gtgcCTGGACACCGACCGCCAGCACGTAGAACTTACCGATa                                  >  1:1233907/1‑41 (MQ=255)
                                                                     tCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCAt                    <  1:2924136/52‑1 (MQ=255)
                                                                     tCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCgg                 <  1:425249/55‑1 (MQ=255)
                                                                     tCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCAgaga  <  1:473949/70‑1 (MQ=255)
                                                                     |                                                                     
CGCGCAGGTAGTAGTAGAGGCCGATTGCCGAACCGACAACCACGGCACCCACCAGCCACCACAAGTGTGTCTGGACACCGACCGCCAGCACGTAGAACTTACCGATAAAGCCCAGCGTCATCGGGATACCGGCCAGAGA  >  minE/1486210‑1486348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A