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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 833,163 G→C 13.3% V541L (GTC→CTC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE833,1630GC13.3% 151.6 / 13.5 60V541L (GTC→CTC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (37/15);  new base C (4/4);  total (41/19)
Fisher's exact test for biased strand distribution p-value = 2.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGATTATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGC  >  minE/833094‑833226
                                                                     |                                                               
cAGATTATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgt                                                                <  1:530504/71‑1 (MQ=255)
cAGATTATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgt                                                                <  1:1469768/71‑1 (MQ=255)
cAGATTATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgt                                                                <  1:3299636/71‑1 (MQ=255)
   attattCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCgg                                                             <  1:1306554/71‑1 (MQ=255)
       ttCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCg                                                         <  1:296428/71‑1 (MQ=255)
         accATCGCCCGTGAATTTGCCGATACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCagg                                                       <  1:1490025/69‑1 (MQ=255)
          gCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCtgg                                                       <  1:1212568/70‑1 (MQ=255)
          gCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCggg                                                       <  1:3083936/70‑1 (MQ=255)
          ccATCGCCCGTGAATTTGCCGCTACCGCCCATAAAACGCATGGGCGCTCGATGATTATCCTCGGCGCaggt                                                      >  1:843456/2‑70 (MQ=255)
            aTCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCt                                                    <  1:1204109/71‑1 (MQ=255)
              cGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgtc                                                               >  1:557628/1‑58 (MQ=255)
               gCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGaa                                                 >  1:879762/1‑71 (MQ=255)
               gCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGa                                                  <  1:3474469/70‑1 (MQ=255)
               gCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGa                                                  <  1:3593080/70‑1 (MQ=255)
               gCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGa                                                  <  1:742685/70‑1 (MQ=255)
                   gTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgtc                                                               <  1:1534219/53‑1 (MQ=255)
                   gTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgt                                                                >  1:620164/1‑52 (MQ=255)
                     gAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTg                                           >  1:718416/1‑71 (MQ=255)
                      aaTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGc                                                     >  1:1520512/1‑60 (MQ=255)
                       aTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTgg                                          >  1:139358/1‑70 (MQ=255)
                       aTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTgg                                          >  1:3614234/1‑70 (MQ=255)
                       aTTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTgg                                          >  1:1775315/1‑70 (MQ=255)
                           gCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCa                                     >  1:2474027/1‑71 (MQ=255)
                           gCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCa                                     >  1:147388/1‑71 (MQ=255)
                               aTAACGCTGATAAAACGCACGGTCGTTCGATGATTAtcgt                                                                <  1:1002676/40‑1 (MQ=255)
                               aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCt                                  >  1:1271685/1‑70 (MQ=255)
                               aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                 <  1:3332809/71‑1 (MQ=255)
                               aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                 >  1:1047353/1‑71 (MQ=255)
                               aTAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                 >  1:1753874/1‑71 (MQ=255)
                                tAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTc                                 >  1:2822664/1‑70 (MQ=255)
                                 aaCGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGa                               >  1:3473686/1‑71 (MQ=255)
                                   cGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCt                                                    >  1:1825987/1‑48 (MQ=255)
                                   cGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCg                                >  1:2847355/1‑68 (MQ=255)
                                   cGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGata                             >  1:187174/1‑71 (MQ=255)
                                    gCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCt                                  <  1:1861822/65‑1 (MQ=255)
                                      tGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATg                           >  1:1678013/1‑70 (MQ=255)
                                        aTAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCgggg                                                      >  1:1118939/1‑41 (MQ=255)
                                        aTAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAAc                        >  1:30463/1‑71 (MQ=255)
                                          aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCgggg                                                      >  1:3726107/1‑39 (MQ=255)
                                          aaaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTa                                        >  1:336373/1‑53 (MQ=255)
                                           aaaCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCt                                                    >  1:1893518/1‑40 (MQ=255)
                                             aCGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCg                   <  1:393827/71‑1 (MQ=255)
                                              cGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGc                                                     >  1:2944199/1‑36 (MQ=255)
                                              cGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGt                  >  1:1435509/1‑71 (MQ=255)
                                               gCATGGGCGCTCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCgcg                 <  1:2385400/71‑3 (MQ=255)
                                                cACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCa                                     >  1:3860512/1‑50 (MQ=255)
                                                cACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTgg                >  1:2284480/1‑71 (MQ=255)
                                                  cGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTc              >  1:61076/1‑71 (MQ=255)
                                                    gTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTg            <  1:3672459/71‑1 (MQ=255)
                                                     tCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCa                                              >  1:2703504/1‑36 (MQ=255)
                                                     tCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCa                                              >  1:3008592/1‑36 (MQ=255)
                                                      cGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCa                                     >  1:455290/1‑44 (MQ=255)
                                                       gctCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGgatgat          >  1:3920848/3‑70 (MQ=255)
                                                       gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGAt          >  1:3471688/1‑70 (MQ=255)
                                                       gTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGAt          >  1:281384/1‑70 (MQ=255)
                                                        ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTAt                                       <  1:1330982/40‑1 (MQ=255)
                                                        ttCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGAt          <  1:296129/69‑1 (MQ=255)
                                                         tCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATgta                         <  1:1583876/53‑3 (MQ=255)
                                                         tCGATGATTATCCTCGGCGCAGGTGTTAACCACTGGTATCa                                     <  1:3749859/41‑1 (MQ=12)
                                                          cGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCa        >  1:241407/1‑69 (MQ=255)
                                                           gatgatTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACa     >  1:3254207/1‑71 (MQ=255)
                                                           gatgatTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCaata     >  1:1961334/1‑69 (MQ=255)
                                                           gatgatTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGATCaata     >  1:349241/1‑69 (MQ=255)
                                                            atgatTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACAt    >  1:1304343/1‑71 (MQ=255)
                                                              gatTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGat                              >  1:2491208/1‑43 (MQ=255)
                                                              gatTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGc  >  1:1351504/1‑71 (MQ=255)
                                                               atTATCCTCGGCGCAGGTGTTAACCACTGGTATCACATGGACATGAACTACCGCGGGATGAGCAATATGc  <  1:1822440/70‑1 (MQ=255)
                                                                     |                                                               
CAGATTATTCGCATCGCCCGTGAATTTGCCGATAACGCTGATAAAACGCACGGTCGTTCGATGATTATCGTCGGTGCGGGGCTGAACCACTGGTATCACCTCGATATGAACTATCGTGGTCTGATCAACATGC  >  minE/833094‑833226

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