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 836,323 T→C 36.2% Y347Y (TAT→TAC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,3230TC36.2% 68.1 / 73.6 80Y347Y (TAT→TAC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (29/22);  new base C (18/11);  total (47/33)
Fisher's exact test for biased strand distribution p-value = 8.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGG  >  minE/836254‑836388
                                                                     |                                                                 
cGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATc                                                                  <  1:5504348/71‑1 (MQ=255)
   acaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGca                                                               <  1:1276949/71‑1 (MQ=255)
    cagcagTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGcac                                                              <  1:4454388/71‑1 (MQ=255)
    cagcagTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGcac                                                              <  1:1163351/71‑1 (MQ=255)
       cagTCGACGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACt                                                           >  1:1075077/1‑71 (MQ=255)
        gttCGCCAGTCTACAAAATGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGcacc                                                             >  1:3885699/3‑67 (MQ=255)
            gCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGcc                                                        >  1:62041/1‑69 (MQ=255)
            gCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                                      <  1:1814838/71‑1 (MQ=255)
            gCCAGTCTACAATATGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGa                                                      <  1:4152390/71‑1 (MQ=255)
               ggTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATgg                                                   >  1:1938163/1‑71 (MQ=255)
                 tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg                                                                 <  1:1365978/55‑1 (MQ=255)
                 tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg                                                                 <  1:462214/55‑1 (MQ=255)
                 tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg                                                                 <  1:1955855/55‑1 (MQ=255)
                 tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCacac                                                            >  1:5177414/1‑60 (MQ=255)
                  ttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCt                                                >  1:3313728/1‑71 (MQ=255)
                   tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                                               >  1:3339406/4‑71 (MQ=255)
                   tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                                               >  1:2633138/4‑71 (MQ=255)
                   tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                                               >  1:5603427/4‑71 (MQ=255)
                     taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                                              >  1:2601604/1‑70 (MQ=255)
                     taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGt                                             <  1:4416471/71‑1 (MQ=255)
                     taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGt                                             <  1:2329371/71‑1 (MQ=255)
                       aaaTGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCg                                                       >  1:3084986/1‑59 (MQ=255)
                       aaaTGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTAc                                           >  1:5058895/1‑71 (MQ=255)
                         aTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGt                                         <  1:1080605/71‑1 (MQ=255)
                            gcgatggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcc                                      <  1:5669701/68‑1 (MQ=255)
                            gcgatggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcc                                      <  1:5044755/68‑1 (MQ=255)
                            gcgatggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcc                                      <  1:3009233/68‑1 (MQ=255)
                              aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                                      <  1:3671006/53‑1 (MQ=255)
                              aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                                      <  1:2309694/53‑1 (MQ=255)
                              aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                                      <  1:5294670/53‑1 (MQ=255)
                              aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                                      <  1:1083093/53‑1 (MQ=255)
                               atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGa                                                      <  1:705400/52‑1 (MQ=16)
                               atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctcc                                   >  1:279153/1‑71 (MQ=255)
                               atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctcc                                   >  1:5123859/1‑71 (MQ=255)
                                tggactggaaACTTGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCt                                                <  1:5275028/57‑1 (MQ=255)
                                tggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctccg                                  >  1:3783667/1‑70 (MQ=255)
                                tggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctccg                                  <  1:3273596/71‑2 (MQ=255)
                                tggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                                              >  1:3175924/1‑59 (MQ=255)
                                 ggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTc                                                 >  1:2866663/1‑55 (MQ=255)
                                 ggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTc                                                 >  1:5430612/1‑55 (MQ=255)
                                 ggactggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctccgc                                 >  1:4979004/1‑69 (MQ=255)
                                 ggaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCct                                  >  1:5205541/1‑70 (MQ=255)
                                  gaatggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCctct                                <  1:4974303/71‑1 (MQ=255)
                                  gaatggaaACTGGCGCTGCCGATGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCctct                                <  1:4317579/71‑1 (MQ=255)
                                   actggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctccg                                  <  1:3774462/66‑2 (MQ=255)
                                   actggaaACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctccg                                  <  1:4182559/66‑2 (MQ=255)
                                    atggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGt                                             <  1:577697/56‑1 (MQ=255)
                                     tggaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                                              <  1:5379786/54‑1 (MQ=255)
                                      ggaaACTGGCGCTGCCGCTGCATCCGGAATATCGcaca                                                             >  1:2064657/1‑38 (MQ=255)
                                      ggaaACTGGCGCTGCCGCTGCATCCGGAATATCGcaca                                                             >  1:1590962/1‑38 (MQ=255)
                                       gaaACTGGCGCTGCCGCTGCATCCGGAATATCGca                                                               >  1:85588/1‑35 (MQ=255)
                                       gaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACTCTGCCGATGGTCTGGTACGTGCCGCCTCTGtctc                           >  1:898755/1‑71 (MQ=255)
                                       gaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                                              >  1:3443953/1‑52 (MQ=255)
                                       gaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                                              >  1:2337142/1‑52 (MQ=255)
                                       gaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGtctc                           >  1:1106516/1‑71 (MQ=255)
                                         aaCTGGCGCTGCCGCTGCAT‑CGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGa                        >  1:1745074/1‑71 (MQ=255)
                                          aCTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGa                        >  1:3532809/1‑71 (MQ=255)
                                          aCTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGa                        >  1:2629192/1‑71 (MQ=255)
                                           cTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGAt                       >  1:3961595/1‑71 (MQ=255)
                                            tGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCt                                                >  1:2142462/1‑45 (MQ=255)
                                              gcgcTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTc                     <  1:3956426/70‑1 (MQ=255)
                                                 ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGt                                         >  1:1070251/1‑47 (MQ=255)
                                                 ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGt                                         >  1:422009/1‑47 (MQ=255)
                                                 ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTc                 <  1:798081/71‑1 (MQ=255)
                                                 ctgccgctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTc                 <  1:1295124/71‑1 (MQ=255)
                                                 ctaccgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTc                 <  1:3645200/68‑1 (MQ=255)
                                                   accgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTcc                >  1:5270579/2‑69 (MQ=255)
                                                   accgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTcc                >  1:3151648/2‑69 (MQ=255)
                                                    ccgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTccta              >  1:1899481/1‑68 (MQ=255)
                                                    ccgttgcACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTccta              >  1:1586877/1‑68 (MQ=255)
                                                      gctgcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcag            >  1:5023683/1‑71 (MQ=255)
                                                         gcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcag            >  1:2268040/1‑68 (MQ=255)
                                                         gcATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTgcag            >  1:5697420/1‑68 (MQ=255)
                                                           aTCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAc       <  1:1530561/71‑1 (MQ=255)
                                                             ccGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc     >  1:5116879/1‑71 (MQ=255)
                                                             ccGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgc     >  1:4999635/1‑71 (MQ=255)
                                                              cGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcgcg    >  1:4769901/1‑71 (MQ=255)
                                                                gAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcg      >  1:1222459/1‑67 (MQ=255)
                                                                gAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGAcg      >  1:1221790/1‑67 (MQ=255)
                                                                gAATACCGCACCCTGCCGATGGTCTGGTACGTTCCTCCGCTGTCACCGATTCAGTCCTACGCAGATGCggg  >  1:3054384/1‑71 (MQ=255)
                                                                   tatCGCACACTGCCGATGGTCTGGTACGTGCCGCctc                                 <  1:4178565/37‑1 (MQ=255)
                                                                     |                                                                 
CGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTCAGTCTGCAGCAGACGCGGG  >  minE/836254‑836388

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