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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 836,749 C→T 27.9% T489T (ACC→ACT) ‡ narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,7490CT27.9% 101.9 / 44.1 68T489T (ACC→ACT) ‡narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (24/25);  new base T (12/7);  total (36/32)
Fisher's exact test for biased strand distribution p-value = 4.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GAAGCCTTCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCA  >  minE/836684‑836818
                                                                 |                                                                     
gAAGCCTTCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAAt                                                                   >  1:1311103/1‑70 (MQ=255)
      ttCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCt                                                            >  1:5374951/1‑71 (MQ=255)
      ttCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCt                                                            >  1:1639148/1‑71 (MQ=255)
        cccGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCa                                                                >  1:2921608/1‑65 (MQ=255)
         ccGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAAtat                                                            <  1:36201/68‑3 (MQ=255)
            gagaAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCaa                                                      <  1:1179091/71‑1 (MQ=255)
            gagaAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCaa                                                      <  1:4171227/71‑1 (MQ=255)
             agaAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAAc                                                     <  1:2411600/71‑1 (MQ=255)
                aaaaTGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGc                                                  >  1:3696734/1‑71 (MQ=255)
                   aTGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCcgt                                               <  1:1872508/71‑1 (MQ=255)
                    tGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCcgtc                                              <  1:5382576/71‑1 (MQ=255)
                    cggCTGCGGTTTTACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                      <  1:455325/62‑1 (MQ=255)
                    cggCTGCGGTTTTACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                      <  1:559492/62‑1 (MQ=255)
                      gCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCcgtcg                                             >  1:2837936/1‑70 (MQ=255)
                      gCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCcgtcg                                             <  1:166639/70‑1 (MQ=255)
                          cGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTAt                                          <  1:5664473/69‑1 (MQ=255)
                             ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCt                                                            <  1:135681/47‑1 (MQ=12)
                             ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                      <  1:4524248/53‑1 (MQ=255)
                             ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                      <  1:1566295/53‑1 (MQ=255)
                             ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                      <  1:503579/53‑1 (MQ=255)
                             cTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATg                                     >  1:3789776/1‑71 (MQ=255)
                             cTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATg                                     >  1:2882609/1‑71 (MQ=255)
                              tttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGc                                    >  1:5645257/1‑71 (MQ=255)
                              tttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGc                                    >  1:1247521/1‑71 (MQ=255)
                               ttACCTTTGGTGATGGCTGCCACGGTTCAGATACCaaa                                                                    >  1:5224641/1‑38 (MQ=255)
                               ttACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCa                                                                <  1:3268082/42‑1 (MQ=255)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCaac                                                              >  1:2580879/1‑43 (MQ=12)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGt                                                          >  1:3234015/1‑48 (MQ=12)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGa                                       >  1:5199273/1‑67 (MQ=255)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGa                                       >  1:4812277/1‑67 (MQ=255)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGc                                    >  1:1749722/1‑70 (MQ=255)
                               ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGc                                    >  1:1399900/1‑70 (MQ=255)
                                 aCCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCAt                                 >  1:3829882/1‑71 (MQ=255)
                                  ccTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                >  1:629293/1‑71 (MQ=255)
                                  ccTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCAt                                 >  1:890104/1‑70 (MQ=255)
                                  ccTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCAt                                 >  1:2334146/1‑70 (MQ=255)
                                   cTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCg                               <  1:3580117/71‑1 (MQ=255)
                                   cTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCg                               <  1:4851786/71‑1 (MQ=255)
                                    tttGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGa                              >  1:4820286/1‑71 (MQ=255)
                                     ttGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTc                                                        <  1:4573182/44‑1 (MQ=255)
                                     ttGGTGATGGCTGACACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                             >  1:4055775/1‑71 (MQ=255)
                                     ttGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCATcaa                              >  1:812827/1‑68 (MQ=255)
                                      tGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCATcaac                             <  1:1709982/70‑4 (MQ=255)
                                        gTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAtgt                           <  1:330699/70‑1 (MQ=255)
                                        gTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAtgt                           <  1:2375236/70‑1 (MQ=255)
                                        gTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAtgt                           >  1:4309356/1‑70 (MQ=255)
                                              gCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAg                     >  1:4026836/1‑70 (MQ=255)
                                               cTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATc                                         <  1:4582762/49‑1 (MQ=255)
                                               cTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATc                                         <  1:716228/49‑1 (MQ=255)
                                                 gCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGa                                       >  1:2145847/1‑49 (MQ=255)
                                                  ccACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGc                                    >  1:1045964/1‑51 (MQ=255)
                                                  ccACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCaa                  <  1:3848394/69‑1 (MQ=255)
                                                   cACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCaaaa                >  1:2136498/1‑70 (MQ=255)
                                                   cACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAAc               <  1:3058433/71‑1 (MQ=255)
                                                   cACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATCCCATCGATGTGACCAGCaaaa                >  1:128532/1‑70 (MQ=255)
                                                     cGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGc                    >  1:3199538/1‑64 (MQ=255)
                                                     cGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACgg             <  1:2870932/71‑1 (MQ=255)
                                                      ggTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCGGCAAAACGGa            <  1:5431492/71‑1 (MQ=255)
                                                       gTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:5630494/50‑1 (MQ=255)
                                                        ttCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGa                                       >  1:299193/1‑42 (MQ=255)
                                                          cAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAtg                            >  1:1454265/1‑51 (MQ=255)
                                                            gATACCAAATTCAATCTGTTCAACAGCCGTCGTATc                                         <  1:5222642/36‑1 (MQ=255)
                                                            gATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:2853566/45‑1 (MQ=255)
                                                             aTACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:300315/44‑1 (MQ=255)
                                                             aTACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:367954/44‑1 (MQ=255)
                                                               aCCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGa                              >  1:2860480/1‑44 (MQ=255)
                                                               aCCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATc    >  1:3407759/1‑70 (MQ=255)
                                                               aCCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATc    >  1:4385657/1‑70 (MQ=255)
                                                                ccAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:1058943/41‑1 (MQ=255)
                                                                ccAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATc                                <  1:3684094/41‑1 (MQ=255)
                                                                ccAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATcc   <  1:1749367/70‑1 (MQ=255)
                                                                ccAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCa  >  1:5092478/1‑71 (MQ=255)
                                                                ccAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCa  >  1:1329710/1‑71 (MQ=255)
                                                                 cAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                             >  1:3869012/1‑43 (MQ=255)
                                                                 cAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                             >  1:3497106/1‑43 (MQ=255)
                                                                 cAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                             >  1:1751439/1‑43 (MQ=255)
                                                                 |                                                                     
GAAGCCTTCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCA  >  minE/836684‑836818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A