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 836,758 T→C 24.7% N492N (AAT→AAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,7580TC24.7% 137.0 / 45.6 81N492N (AAT→AAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (29/32);  new base C (12/8);  total (41/40)
Fisher's exact test for biased strand distribution p-value = 4.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCATGA  >  minE/836690‑836821
                                                                    |                                                               
ttCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCt                                                               >  1:5374951/1‑71 (MQ=255)
ttCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCt                                                               >  1:1639148/1‑71 (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                                                <  1:166639/70‑1 (MQ=255)
                gCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCcgtcg                                                >  1:2837936/1‑70 (MQ=255)
                    cGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTAt                                             <  1:5664473/69‑1 (MQ=255)
                       ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCt                                                               <  1:135681/47‑1 (MQ=12)
                       ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                         <  1:4524248/53‑1 (MQ=255)
                       ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                         <  1:503579/53‑1 (MQ=255)
                       ttttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCaa                                                         <  1:1566295/53‑1 (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)
                         ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGt                                                             >  1:3234015/1‑48 (MQ=12)
                         ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGa                                          >  1:4812277/1‑67 (MQ=255)
                         ttACCTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGa                                          >  1:5199273/1‑67 (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                                    >  1:2334146/1‑70 (MQ=255)
                            ccTTTGGCGACGGTTGCCACGGTTCGGACAGTAAATTCAACCTGTTCAACAGTAGCCGTATCGATGCCAt                                    >  1:890104/1‑70 (MQ=255)
                             cTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCg                                  <  1:4851786/71‑1 (MQ=255)
                             cTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCg                                  <  1:3580117/71‑1 (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                              >  1:4309356/1‑70 (MQ=255)
                                  gTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAtgt                              <  1:2375236/70‑1 (MQ=255)
                                        gCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAg                        >  1:4026836/1‑70 (MQ=255)
                                         cTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATc                                            <  1:716228/49‑1 (MQ=255)
                                         cTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATc                                            <  1:4582762/49‑1 (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       >  1:4385657/1‑70 (MQ=255)
                                                         aCCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATc       >  1:3407759/1‑70 (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                                >  1:1751439/1‑43 (MQ=255)
                                                           cAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                                >  1:3497106/1‑43 (MQ=255)
                                                           cAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGAt                                >  1:3869012/1‑43 (MQ=255)
                                                            aaaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCa         >  1:1214244/1‑65 (MQ=255)
                                                            aaaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCATg   <  1:3233404/71‑1 (MQ=255)
                                                            aaaTTCAACCTGTTCAACAGTAGCCGTATCGATGc                                       >  1:5453585/1‑35 (MQ=19)
                                                             aaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAATACgg                <  1:4772659/57‑1 (MQ=255)
                                                             aaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACgg                <  1:1474416/57‑1 (MQ=255)
                                                             aaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACgg                <  1:1290494/57‑1 (MQ=255)
                                                             aaTTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCATGa  >  1:4456266/1‑71 (MQ=255)
                                                              aTTCAACCTGTTCAACAGTAGCCGTATCGATGCCATc                                   <  1:2306834/37‑1 (MQ=25)
                                                                tCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCaaaa                   >  1:798479/1‑51 (MQ=255)
                                                                   aTCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCaa                     <  1:1959302/46‑1 (MQ=255)
                                                                   aTCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCaa                     <  1:5214504/46‑1 (MQ=255)
                                                                    |                                                               
TTCCCGGAGAAAAATGGCTGCGGCTTTACCTTTGGTGATGGCTGCCACGGTTCAGATACCAAATTCAATCTGTTCAACAGCCGTCGTATCGATGCCATCGATGTGACCAGCAAAACGGAGCCGCATCCATGA  >  minE/836690‑836821

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