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 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 753,855 T→C 51.1% N189S (AAC→AGC)  ycfT ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE753,8550TC51.1% 2.2 / 136.9 92N189S (AAC→AGC) ycfTpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (26/19);  new base C (26/21);  total (52/40)
Fisher's exact test for biased strand distribution p-value = 8.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

ACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAG  >  minE/753788‑753922
                                                                   |                                                                   
acaGGTCATTATTGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCa                                                                  <  1:1041803/71‑1 (MQ=255)
acaGGTAATTATTGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCa                                                                  >  1:2767517/1‑71 (MQ=255)
  aGGTCATTATTGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCAt                                                                 <  1:1944292/70‑1 (MQ=255)
       attattGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCcca                                                           >  1:2316614/1‑71 (MQ=255)
         tattGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCccac                                                          >  1:2237335/1‑70 (MQ=255)
          attGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCccacca                                                        >  1:3291180/1‑71 (MQ=255)
           ttgttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCcaccac                                                       <  1:982639/71‑1 (MQ=255)
           ttgttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCcaccac                                                       <  1:944791/71‑1 (MQ=255)
           ttgttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCcaccac                                                       <  1:695000/71‑1 (MQ=255)
           ttgttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCccac                                                          <  1:2544512/68‑1 (MQ=255)
            tgttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCcaccac                                                       <  1:2270086/70‑1 (MQ=255)
             gttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGt                                                                     >  1:1641178/1‑55 (MQ=255)
             gttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGt                                                                     >  1:2968385/1‑55 (MQ=255)
              ttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCa                                                                  <  1:1540727/57‑1 (MQ=255)
              ttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCa                                                                  <  1:559461/57‑1 (MQ=255)
              ttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCa                                                                  <  1:487604/57‑1 (MQ=255)
              ttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCa                                                                  <  1:742374/57‑1 (MQ=255)
              ttgCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCa                                                                  <  1:2600336/57‑1 (MQ=255)
                gcgcCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGt                                                  >  1:3671398/1‑71 (MQ=255)
                 cgcCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGt                                                  <  1:765682/70‑1 (MQ=255)
                 cgcCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTAATTCCCCACCACGGCGt                                                  <  1:329997/70‑1 (MQ=255)
                   ccAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCg                                                   <  1:3310761/67‑1 (MQ=255)
                   ccAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTg                                                 >  1:1661210/1‑69 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTc                                                                   >  1:1242477/1‑50 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCa                                                                  >  1:637928/1‑51 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCa                                                                  >  1:3302958/1‑51 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTc                                                               >  1:1197400/1‑54 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTc                                                               >  1:1652768/1‑54 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGa                                              <  1:2348655/71‑1 (MQ=255)
                    cAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACAATGCTCATTc                                                               >  1:1214273/1‑54 (MQ=255)
                     aaaCCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTc                                                                   >  1:1400853/1‑49 (MQ=255)
                     aaaCCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTgg                                                >  1:3391149/1‑68 (MQ=255)
                      aaCCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAAc                                            >  1:3369017/1‑71 (MQ=255)
                      aaCCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAAc                                            >  1:1959347/1‑71 (MQ=255)
                           tGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTcccc                                                            >  1:3496980/1‑50 (MQ=255)
                           tGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTcccc                                                            >  1:1867928/1‑50 (MQ=255)
                           tGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTcccc                                                            >  1:2376950/1‑50 (MQ=255)
                           tGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTcccc                                                            >  1:1778318/1‑50 (MQ=255)
                           tGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGT‑GGAACGAAAt                                       <  1:2719873/70‑1 (MQ=255)
                            gcgcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAAt                                       >  1:642673/1‑70 (MQ=255)
                             cgcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAAtt                                      <  1:3729189/70‑1 (MQ=255)
                             cgcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAAtt                                      <  1:276030/70‑1 (MQ=255)
                             cgcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAAtt                                      <  1:1589951/70‑1 (MQ=255)
                              gcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTaa                                    <  1:194458/71‑1 (MQ=255)
                              gcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTg                                                 <  1:1180650/58‑1 (MQ=255)
                              gcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTg                                                 <  1:502807/58‑1 (MQ=255)
                              gcCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTg                                                 <  1:2314104/58‑1 (MQ=255)
                                  aGGCTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGc                                >  1:3452068/1‑71 (MQ=255)
                                    gCTGTAATATGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGa                                          <  1:1992204/59‑1 (MQ=255)
                                     cTGTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCca                              >  1:1632074/1‑70 (MQ=255)
                                      tGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGa                                          <  1:2822333/57‑1 (MQ=255)
                                       gTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCcaca                            >  1:2180941/1‑70 (MQ=255)
                                       gTAATAAGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCacac                           >  1:1916046/1‑71 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:1606184/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:62177/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:1610545/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:556250/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:3180000/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTccc                                                             >  1:322812/1‑36 (MQ=255)
                                        taataaGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTa                                     <  1:2468057/60‑1 (MQ=255)
                                         aataaGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGc                                >  1:3089096/1‑64 (MQ=255)
                                         aataaGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGc                                >  1:3379981/1‑64 (MQ=255)
                                         aataaGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACt                          >  1:2397562/1‑70 (MQ=255)
                                          ataaGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTca                        <  1:631295/71‑1 (MQ=255)
                                            aaGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:3167667/1‑70 (MQ=255)
                                             aGGCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGc                                <  1:756484/60‑1 (MQ=255)
                                              ggCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcagcag                    >  1:2131973/1‑71 (MQ=255)
                                              ggCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcagcag                    <  1:2440447/71‑1 (MQ=255)
                                              ggCAAATTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAAt                                       >  1:672135/1‑52 (MQ=255)
                                               gCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGt                                                  <  1:1583676/40‑1 (MQ=255)
                                               gCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGt                                                  <  1:2836533/40‑1 (MQ=255)
                                               gCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGt                                                  <  1:1988138/40‑1 (MQ=255)
                                               gCAAATTGCGGATCACACTGTTCATTCCCCAACACGGCGt                                                  <  1:2447146/40‑1 (MQ=255)
                                                  aaTTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTac                 >  1:63429/1‑70 (MQ=255)
                                                  aaTTGCGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTac                 >  1:1522871/1‑70 (MQ=255)
                                                   aTTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTaca                >  1:2552764/1‑70 (MQ=255)
                                                   aTTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTaca                >  1:1998719/1‑70 (MQ=255)
                                                       cGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTacaaaca            <  1:726476/70‑1 (MQ=255)
                                                       cGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTacaaaca            <  1:3101919/70‑1 (MQ=255)
                                                       cGGATCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTacaaaca            <  1:3449945/70‑1 (MQ=255)
                                                          aTCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGc        <  1:575554/71‑1 (MQ=255)
                                                           tCACACTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGCg       <  1:2516461/71‑1 (MQ=255)
                                                            cacaCTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGt                   >  1:954116/1‑58 (MQ=255)
                                                            cacaCTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGt                   >  1:3727278/1‑58 (MQ=255)
                                                              cacTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCcaca                            >  1:3426951/1‑47 (MQ=255)
                                                              cacTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAACCAAGGCGaa     >  1:3267836/1‑70 (MQ=255)
                                                              cacTGCTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGc        <  1:2351409/67‑1 (MQ=255)
                                                                cTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGc                                >  1:1403424/1‑41 (MQ=255)
                                                                cTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAg  >  1:1407985/1‑71 (MQ=255)
                                                                  gTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:2826742/1‑48 (MQ=255)
                                                                  gTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:716846/1‑48 (MQ=255)
                                                                  gTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:1736386/1‑48 (MQ=255)
                                                                  gTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:1980223/1‑48 (MQ=255)
                                                                  gTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTcag                       >  1:456228/1‑48 (MQ=255)
                                                                   |                                                                   
ACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGGCTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACGAAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAG  >  minE/753788‑753922

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