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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,262,618 C→T 44.3% intergenic (‑227/+186) rplJ ← / ← rplA 50S ribosomal subunit protein L10/50S ribosomal subunit protein L1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,262,6180CT44.3% 54.6 / 163.7 122intergenic (‑227/+186)rplJ/rplA50S ribosomal subunit protein L10/50S ribosomal subunit protein L1
Reads supporting (aligned to +/- strand):  ref base C (31/37);  new base T (27/27);  total (58/64)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01

Only 100 of 122 total aligned reads displayed.

AAACTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTATGCT  >  minE/2262554‑2262685
                                                                |                                                                   
aaaCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGc                                                               >  1:3139698/1‑71 (MQ=255)
aaaCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGc                                                               >  1:2008452/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTa                                                             >  1:3472769/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTa                                                             >  1:3467864/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTa                                                             >  1:3949991/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTa                                                             >  1:3442572/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTa                                                             >  1:4077552/1‑71 (MQ=255)
  aCTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTa                                                             >  1:2563192/1‑71 (MQ=255)
      cTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTc                                                          <  1:638948/70‑1 (MQ=255)
      cTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTc                                                          <  1:4133027/70‑1 (MQ=255)
      cTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTc                                                          <  1:1899460/70‑1 (MQ=255)
      cTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTc                                                          <  1:1549216/70‑1 (MQ=255)
      cTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTc                                                          <  1:3204532/70‑1 (MQ=255)
         cGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCt                                                      >  1:3337569/1‑71 (MQ=255)
         cGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCt                                                      <  1:3476346/71‑1 (MQ=255)
         cGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCt                                                      <  1:3589828/71‑1 (MQ=255)
         cGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCt                                                      <  1:3877335/71‑1 (MQ=255)
         cGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCt                                                      <  1:3709879/71‑1 (MQ=255)
            tCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:4216531/71‑1 (MQ=255)
            tCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTtgt                                                   <  1:845034/71‑1 (MQ=255)
             cTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCa                                                         >  1:755305/1‑64 (MQ=255)
             cTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCa                                                         >  1:352981/1‑64 (MQ=255)
              ttCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGa                                                 >  1:1150404/1‑71 (MQ=255)
                cGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACg                                               >  1:3999784/1‑71 (MQ=255)
                  aCGGAGGCCTGGATAGGCGAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGc                                             <  1:3116270/71‑1 (MQ=255)
                  aCGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGc                                             <  1:2114920/71‑1 (MQ=255)
                  aCGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGc                                             <  1:2181603/71‑1 (MQ=255)
                  aCGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGc                                             <  1:2312448/71‑1 (MQ=255)
                    ggAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGt                                           >  1:1852429/1‑71 (MQ=255)
                    ggAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGt                                           >  1:3140158/1‑71 (MQ=255)
                     gAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGtt                                          >  1:3211794/1‑71 (MQ=255)
                       ggCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTgg                                        >  1:2992846/1‑71 (MQ=255)
                       ggCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTgg                                        >  1:1726755/1‑71 (MQ=255)
                       ggCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTg                                         >  1:838259/1‑70 (MQ=255)
                           tGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTtgt                                                   <  1:660952/56‑1 (MQ=255)
                           tGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTtgt                                                   <  1:1303261/56‑1 (MQ=255)
                           tGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACgg                                              <  1:4166707/61‑1 (MQ=255)
                           tGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACgg                                              <  1:3399560/61‑1 (MQ=255)
                             gATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGa                                                 >  1:3526686/1‑56 (MQ=255)
                             gATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGa                                                 >  1:1594534/1‑56 (MQ=255)
                             gATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGa                                                 >  1:1796932/1‑56 (MQ=255)
                             gATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCg                                            >  1:2142683/1‑61 (MQ=255)
                             gATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCg                                            >  1:3921209/1‑61 (MQ=255)
                               tAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGcttcctt                                 >  1:2674767/1‑70 (MQ=255)
                                 ggCCAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCa                               <  1:907341/70‑1 (MQ=255)
                                 ggCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCa                               <  1:551433/70‑1 (MQ=255)
                                 ggCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCAt                              <  1:2710854/71‑1 (MQ=255)
                                    cAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:4072936/71‑1 (MQ=255)
                                    cAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:1090941/71‑1 (MQ=255)
                                    cAGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:2145739/71‑1 (MQ=255)
                                     aGGCTCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:640318/70‑1 (MQ=255)
                                      ggCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGc                                             <  1:2435917/51‑1 (MQ=255)
                                       gCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        <  1:4248308/71‑1 (MQ=255)
                                       gCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        <  1:2718153/71‑1 (MQ=255)
                                        cTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        >  1:1383343/1‑70 (MQ=255)
                                        cTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        >  1:3647861/1‑70 (MQ=255)
                                         tCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:2947311/42‑1 (MQ=255)
                                         tCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:1505943/42‑1 (MQ=255)
                                         tCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:825366/42‑1 (MQ=255)
                                         tCCAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:899730/42‑1 (MQ=255)
                                         tCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        >  1:722691/1‑69 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:2567856/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:2694916/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:3311988/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:3600828/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:1071251/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:1202826/40‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGa                                                 >  1:1587774/1‑42 (MQ=255)
                                           cAACGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGt                    <  1:3183914/71‑1 (MQ=255)
                                           cAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGt                                           >  1:267687/1‑48 (MQ=255)
                                           cAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGt                                           >  1:1770694/1‑48 (MQ=255)
                                             aCGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTca                  >  1:2467834/1‑71 (MQ=255)
                                             aCGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTca                  >  1:2799332/1‑71 (MQ=255)
                                             aCGAACAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGGca                  >  1:3294920/1‑71 (MQ=255)
                                              cGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGc                                             <  1:268291/43‑1 (MQ=255)
                                               gAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTg                                         <  1:4207843/46‑1 (MQ=255)
                                                aaCAAATCTTTTCTATTCGTCGCTATTCAGCTtgt                                                   <  1:3953730/35‑1 (MQ=255)
                                                aaCAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACAt               <  1:2563545/71‑1 (MQ=255)
                                                 aCAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTcaca                >  1:734699/1‑69 (MQ=255)
                                                 aCAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTcaca                >  1:1251288/1‑69 (MQ=255)
                                                 aCAAATCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTcaca                >  1:1263795/1‑69 (MQ=255)
                                                 aCAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGc                                       >  1:2263769/1‑46 (MQ=255)
                                                 aCAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGc                                       >  1:3726772/1‑46 (MQ=255)
                                                  cAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:2136848/57‑1 (MQ=255)
                                                  cAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCg                           <  1:3837447/57‑1 (MQ=255)
                                                    aaTCTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATa              <  1:93713/68‑1 (MQ=255)
                                                    aaTCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGtt           <  1:2277566/71‑1 (MQ=255)
                                                    aaTCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGtt           <  1:2907845/71‑1 (MQ=255)
                                                       cTTTTCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCa                         >  1:3406001/1‑54 (MQ=255)
                                                        ttttCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGcttcctt                                 <  1:4186979/45‑1 (MQ=255)
                                                        ttttCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGc        >  1:1217421/1‑70 (MQ=255)
                                                          ttCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTAt     >  1:1362328/1‑71 (MQ=255)
                                                          ttCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTAt     >  1:1931135/1‑71 (MQ=255)
                                                          ttCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTAt     >  1:2550898/1‑71 (MQ=255)
                                                          ttCTATTCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTAt     >  1:2884953/1‑71 (MQ=255)
                                                          ttCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGc        <  1:4118074/68‑1 (MQ=255)
                                                            cTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGc        <  1:1443257/66‑1 (MQ=255)
                                                            cTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTATGc   >  1:2897516/1‑71 (MQ=255)
                                                               tCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCAc                        <  1:3919194/47‑1 (MQ=255)
                                                               tCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTATGCt  <  1:1504192/69‑1 (MQ=255)
                                                                |                                                                   
AAACTCCTGCGGTCTTCGACGGAGGCCTGGATAGGCCAGGCTCCAACGAACAAATCTTTTCTATCCGTCGCTATTCAGCTTGTGACGGCGTTGGCTTCCTTCATTCGCACCAGTCACATAGTTAGCTATGCT  >  minE/2262554‑2262685

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