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 836,302 G→A 37.3% A340A (GCG→GCA)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,3020GA37.3% 70.7 / 69.0 75A340A (GCG→GCA) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base G (23/24);  new base A (13/15);  total (36/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TTCCGCTGAGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTC  >  minE/836232‑836369
                                                                      |                                                                   
ttCCGCTGAGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGgcg                                                                     <  1:3288644/71‑1 (MQ=255)
     cTGAGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGcgctgcc                                                                >  1:526092/1‑71 (MQ=255)
        aGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGcgctgccgct                                                             >  1:3569823/1‑71 (MQ=255)
        aGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGcgctgccgc                                                              >  1:5205604/1‑70 (MQ=255)
            tgaTTGACGCTGCCCAGCGTTCGCCAGTCTACAAAATGGCGATGGACTGGAAACTGGCACTACCGTTGCa                                                          <  1:882684/68‑1 (MQ=255)
              aTTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATcc                                                       >  1:4703232/1‑71 (MQ=255)
                tGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGgcgc                                                                    <  1:2782649/56‑1 (MQ=255)
                   aGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCa                                                          <  1:4263137/63‑1 (MQ=255)
                   aGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCa                                                          <  1:5246044/63‑1 (MQ=255)
                      cGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATc                                               <  1:5504348/71‑1 (MQ=255)
                        cacaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGaa                                                   >  1:1356357/1‑65 (MQ=255)
                         acaGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGca                                            <  1:1276949/71‑1 (MQ=255)
                          cagcagTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGcac                                           <  1:1163351/71‑1 (MQ=255)
                          cagcagTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGcac                                           <  1:4454388/71‑1 (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                                              <  1:1955855/55‑1 (MQ=255)
                                       tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg                                              <  1:462214/55‑1 (MQ=255)
                                       tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCg                                              <  1:1365978/55‑1 (MQ=255)
                                       tttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCacac                                         >  1:5177414/1‑60 (MQ=255)
                                        ttATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCt                             >  1:3313728/1‑71 (MQ=255)
                                         tataAAATGGCAATGGAATGGAAACTGGcgctgccgctgc                                                           >  1:2803711/1‑40 (MQ=255)
                                         tataAAATGGCAATGGAATGGAAACTGGcgctgccgctgc                                                           >  1:4928706/1‑40 (MQ=255)
                                         tataAAATGGCAATGGAATGGAAACTGGcgctgccgctgc                                                           >  1:5595983/1‑40 (MQ=255)
                                         tataAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGaa                                                   >  1:5086200/1‑48 (MQ=255)
                                         tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                            >  1:2633138/4‑71 (MQ=255)
                                         tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                            >  1:5603427/4‑71 (MQ=255)
                                         tacaaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTg                            >  1:3339406/4‑71 (MQ=255)
                                           taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                           >  1:2601604/1‑70 (MQ=255)
                                           taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGt                          <  1:4416471/71‑1 (MQ=255)
                                           taAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGt                          <  1:2329371/71‑1 (MQ=255)
                                            aaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCAccctg                                                     <  1:3262412/43‑3 (MQ=12)
                                            aaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCAccctg                                                     <  1:4885262/43‑3 (MQ=12)
                                            aaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCAccctg                                                     <  1:991576/43‑3 (MQ=12)
                                            aaaaTGGCGATGGACTGGAAACTGGCACTACCGTTGCAccctg                                                     <  1:3595060/43‑3 (MQ=12)
                                             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                   <  1:3009233/68‑1 (MQ=255)
                                                  gcgatggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcc                   <  1:5044755/68‑1 (MQ=255)
                                                   cAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAat                                                  <  1:709536/39‑1 (MQ=255)
                                                   cAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAat                                                  <  1:1162407/39‑1 (MQ=255)
                                                   cAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAat                                                  <  1:2842852/39‑1 (MQ=255)
                                                   cAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAat                                                  <  1:4996949/39‑1 (MQ=255)
                                                    aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                   <  1:1083093/53‑1 (MQ=255)
                                                    aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                   <  1:3671006/53‑1 (MQ=255)
                                                    aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                   <  1:2309694/53‑1 (MQ=255)
                                                    aatggaatggAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGa                                   <  1:5294670/53‑1 (MQ=255)
                                                     atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGa                                   <  1:705400/52‑1 (MQ=16)
                                                     atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctcc                >  1:5123859/1‑71 (MQ=255)
                                                     atggactggaAACTGGCACTACCGTTGCACCCTGAATACCGCACCCTGCCGATGGTCTGGTACGTtcctcc                >  1:279153/1‑71 (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)
                                                        gaatggaaACTGGCGCTGCCGCTGCATCCGGAata                                                 >  1:355919/1‑35 (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                           >  1:2337142/1‑52 (MQ=255)
                                                             gaaACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTgg                           >  1:3443953/1‑52 (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)
                                                                      |                                                                   
TTCCGCTGAGCGTTATTGAAGCCGCACAGCAGTCGCCGGTTTATAAAATGGCAATGGAATGGAAACTGGCGCTGCCGCTGCATCCGGAATATCGCACACTGCCGATGGTCTGGTACGTGCCGCCTCTGTCTCCGATTC  >  minE/836232‑836369

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