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 832,250 T→C 33.3% T236T (ACT→ACC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,2500TC33.3% 78.5 / 61.7 75T236T (ACT→ACC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (28/22);  new base C (11/14);  total (39/36)
Fisher's exact test for biased strand distribution p-value = 3.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCA  >  minE/832180‑832318
                                                                      |                                                                    
cTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACt                                                                      <  1:163062/71‑1 (MQ=255)
    cTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACg                                                                  <  1:1722190/71‑1 (MQ=255)
      tAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGt                                                                 <  1:3375919/70‑1 (MQ=255)
      tAAGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGt                                                                 <  1:3382378/70‑1 (MQ=255)
       aaGTTTCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTa                                                                <  1:1006427/70‑1 (MQ=255)
       aaGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGt                                                                 <  1:4166571/69‑1 (MQ=255)
            tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGaa                                                          >  1:1655704/1‑71 (MQ=255)
            tCTACGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGa                                                           <  1:3303868/70‑1 (MQ=255)
             cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                                                           <  1:999977/69‑1 (MQ=255)
             cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                                                           <  1:2123804/69‑1 (MQ=255)
             cTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                                                         >  1:3042141/1‑71 (MQ=255)
              tACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                                                         >  1:1807426/1‑70 (MQ=255)
              tACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATc                                                        >  1:1283628/1‑71 (MQ=255)
              tACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATc                                                        >  1:1396551/1‑71 (MQ=255)
               aCGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                                                         >  1:4469270/1‑69 (MQ=255)
                cGACTGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATc                                                        <  1:5684819/69‑1 (MQ=255)
                cGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAAt                                                         <  1:90272/68‑1 (MQ=255)
                cGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATct                                                       >  1:4196601/1‑70 (MQ=255)
                   cTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATctgctg                                                   <  1:1065204/71‑1 (MQ=255)
                    tGGTATTGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCgg                                                            <  1:1009180/61‑1 (MQ=255)
                     ggTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGAc                                                 >  1:5140846/1‑71 (MQ=255)
                         ttGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGaa                                                          <  1:2171945/57‑1 (MQ=255)
                         ttGCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAATCTGCCGAc                                                 >  1:1859496/2‑67 (MQ=255)
                         cTGCGTCTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACt                                                <  1:1194552/68‑1 (MQ=255)
                           gCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa                                            >  1:180735/1‑70 (MQ=255)
                           gCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTa                                            >  1:3097322/1‑70 (MQ=255)
                           gCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGa                                                                    >  1:3131241/1‑46 (MQ=255)
                           gCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAAt                                                         >  1:5092699/1‑57 (MQ=255)
                           gCGACCTGCCGCCCGCCTCGCCGATGACCTGGGGCGAGCAAACCGACGTACCGGAAt                                                         >  1:3352922/1‑57 (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)
                                    ctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTa                                                                >  1:4872348/1‑41 (MQ=255)
                                    ctcctGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTa                                                                >  1:4903174/1‑41 (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)
                                              tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGaa                                                          >  1:5625362/1‑37 (MQ=255)
                                              tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGaa                                                          >  1:267698/1‑37 (MQ=255)
                                              tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                                                           <  1:3440159/36‑1 (MQ=255)
                                              tcCGCAAACCTGGGGCGAGCAAACTGACGTACCGGa                                                           <  1:5655540/36‑1 (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                      <  1:5186408/71‑1 (MQ=255)
                                                cGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGcc                      <  1:3036599/71‑1 (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)
                                                                    aCTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCa  <  1:2961473/71‑1 (MQ=255)
                                                                     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         >  1:3295964/1‑62 (MQ=255)
                                                                      tGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACg         >  1:170113/1‑62 (MQ=255)
                                                                      |                                                                    
CTTGCTTAAGCTTCTACGACTGGTACTGCGACTTGCCTCCTGCGTCTCCGCAAACCTGGGGCGAGCAAACTGACGTACCGGAATCTGCTGACTGGTACAACTCCAGCTACATCATCGCCTGGGGGTCAAACGTGCCGCA  >  minE/832180‑832318

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