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 832,268 T→C 37.5% A242A (GCT→GCC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,2680TC37.5% 65.7 / 86.0 88A242A (GCT→GCC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (31/24);  new base C (19/14);  total (50/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATG  >  minE/832199‑832335
                                                                     |                                                                   
cTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                                                                    <  1:1065204/71‑1 (MQ=255)
  ggTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGAc                                                                  >  1:5140846/1‑71 (MQ=255)
      ttGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGAc                                                                  >  1:1859496/2‑67 (MQ=255)
      cTGCGTCTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACt                                                                 <  1:1194552/68‑1 (MQ=255)
        gCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa                                                             >  1:3097322/1‑70 (MQ=255)
        gCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa                                                             >  1:180735/1‑70 (MQ=255)
        gCGACATGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTa                                                             >  1:2420630/1‑70 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTg                                                                >  1:2286052/1‑66 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                            <  1:1238824/70‑1 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTAc                                                            <  1:3566441/70‑1 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACa                                                           <  1:945171/71‑1 (MQ=255)
         cGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACa                                                           <  1:4997379/71‑1 (MQ=255)
          gACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACaa                                                          <  1:3450789/71‑1 (MQ=255)
           aCTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAAc                                                         >  1:3771725/1‑71 (MQ=255)
             ttGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTc                                                       >  1:418955/1‑71 (MQ=255)
                cctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAg                                                    >  1:2857378/1‑71 (MQ=255)
                    ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTa                                                 >  1:3282601/1‑70 (MQ=255)
                    ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTa                                                 >  1:5526511/1‑70 (MQ=255)
                    ctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGATa                                                 >  1:2386521/1‑70 (MQ=255)
                       cGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTAcat                                              >  1:5357351/1‑70 (MQ=255)
                           tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCg                                         >  1:1374314/1‑71 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                          <  1:1900274/68‑1 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                          <  1:3833639/68‑1 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACatcatc                                          <  1:4710229/68‑1 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGcc                                       <  1:3036599/71‑1 (MQ=255)
                             cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGcc                                       <  1:5186408/71‑1 (MQ=255)
                               atgaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTg                                     >  1:1306513/4‑71 (MQ=255)
                                 gaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTggg                                   >  1:3806285/2‑71 (MQ=255)
                                 gaCCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTga                                    <  1:3316019/69‑2 (MQ=255)
                                    cTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGt                                >  1:3091976/1‑71 (MQ=255)
                                    cTGCGGCGAGCAAACTGACGTACCGGAATCTGCTGACTgg                                                               <  1:724092/40‑1 (MQ=255)
                                     tGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                        >  1:5623445/1‑62 (MQ=255)
                                      ggggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGc                                                   >  1:5555730/1‑50 (MQ=255)
                                      ggggCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTata                                                           >  1:1116689/1‑40 (MQ=38)
                                       gggCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCa                              >  1:2219594/1‑70 (MQ=255)
                                       gggCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTct                              >  1:1850287/1‑69 (MQ=255)
                                       gggCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTct                              <  1:3094541/70‑2 (MQ=255)
                                         gCGAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTg                                     <  1:1357902/61‑1 (MQ=255)
                                           gAGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGt                         <  1:4493414/71‑1 (MQ=255)
                                            aGCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCg                                         <  1:998085/54‑1 (MQ=38)
                                             gCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGc                       <  1:383673/71‑1 (MQ=255)
                                             gCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCg                                         <  1:463908/53‑1 (MQ=38)
                                             gCAAACCGACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGtac                       <  1:120337/71‑3 (MQ=255)
                                                aaCTGACGTACTGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                     >  1:2519185/1‑70 (MQ=255)
                                                aaCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCg                     >  1:3401781/1‑70 (MQ=255)
                                                 accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                     >  1:468365/4‑69 (MQ=255)
                                                 accgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCa                   <  1:5522420/68‑1 (MQ=255)
                                                 aCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa                   <  1:2961473/71‑1 (MQ=255)
                                                  ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                      >  1:565916/3‑51 (MQ=38)
                                                  ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                      >  1:2336842/3‑51 (MQ=38)
                                                  ccgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCt                                      >  1:2343359/3‑51 (MQ=38)
                                                  cTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCt                                      >  1:520417/1‑51 (MQ=255)
                                                   tGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                     <  1:5598279/35‑1 (MQ=255)
                                                   tGACGTACCGGAATCTGCTGACTGGTACAACTCCa                                                     <  1:5091767/35‑1 (MQ=255)
                                                   tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTgggg                                  <  1:3502929/54‑1 (MQ=255)
                                                   tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                          >  1:170113/1‑62 (MQ=255)
                                                   tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg                          >  1:3295964/1‑62 (MQ=255)
                                                   cgACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                 >  1:1384451/2‑71 (MQ=255)
                                                    gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                 >  1:5269461/1‑70 (MQ=255)
                                                    gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                 >  1:1956245/1‑70 (MQ=255)
                                                    gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGa                 >  1:781607/1‑70 (MQ=255)
                                                    gACGTACCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGAc                <  1:4100523/71‑1 (MQ=255)
                                                     aCGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcg               >  1:2852621/1‑71 (MQ=255)
                                                         aCCGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                     <  1:3213199/61‑1 (MQ=255)
                                                          ccGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc          >  1:4827136/1‑71 (MQ=255)
                                                          ccGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAc          >  1:2828340/1‑71 (MQ=255)
                                                           cGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGAcgcg             <  1:3832576/67‑1 (MQ=255)
                                                           cGGAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                     <  1:1970589/59‑1 (MQ=38)
                                                            ggAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCg                     <  1:4413453/58‑1 (MQ=38)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCg                                         >  1:3247520/1‑37 (MQ=255)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                        >  1:1041930/1‑38 (MQ=255)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGc                                        >  1:3921026/1‑38 (MQ=255)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc       >  1:676253/1‑71 (MQ=255)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcccc       >  1:2135068/1‑71 (MQ=255)
                                                             gAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAcc         >  1:3576965/1‑69 (MQ=255)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                            >  1:2442026/1‑50 (MQ=38)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                            >  1:938377/1‑50 (MQ=38)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCtaa                            >  1:2908903/1‑50 (MQ=38)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc       <  1:935558/71‑1 (MQ=255)
                                                             gAATCTGCCGACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTAcgcc       <  1:878330/71‑1 (MQ=255)
                                                              aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt            <  1:5454331/65‑1 (MQ=255)
                                                              aaTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGt            <  1:2089654/65‑1 (MQ=255)
                                                               aTCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCgg     <  1:3040704/71‑1 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:2711814/46‑1 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:251050/46‑1 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:519489/46‑1 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc          >  1:240491/1‑65 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc          >  1:127842/1‑65 (MQ=255)
                                                                tCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTAc          >  1:166102/1‑65 (MQ=255)
                                                                 ctgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt   >  1:2694472/1‑71 (MQ=255)
                                                                  tgctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATg  >  1:4384016/1‑71 (MQ=255)
                                                                  tgccgACTGGTATAACTCCAGCTACATCATCGCCTGGGGGTCTAACGTACCGCAGACACGTACGCCGGacg  >  1:3068280/1‑69 (MQ=255)
                                                                   gctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGAt   >  1:1039279/1‑69 (MQ=255)
                                                                   gctgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCACGGAt   >  1:2394206/1‑69 (MQ=255)
                                                                     tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:3941471/41‑1 (MQ=255)
                                                                     tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:5640793/41‑1 (MQ=255)
                                                                     tgACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCaa                             <  1:2425721/41‑1 (MQ=255)
                                                                     |                                                                   
CTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCAGACGCGTACCCCGGATG  >  minE/832199‑832335

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