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 833,898 A→G 21.0% I786V (ATT→GTT)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE833,8980AG21.0% 149.2 / 34.5 76I786V (ATT→GTT) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (38/22);  new base G (9/7);  total (47/29)
Fisher's exact test for biased strand distribution p-value = 7.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GGAAGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCC  >  minE/833828‑833968
                                                                      |                                                                      
ggAAGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGAcatca                                                                        >  1:5251164/1‑71 (MQ=255)
 gAAGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGAcatcat                                                                       >  1:5199391/1‑71 (MQ=255)
 gAAGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGAcatca                                                                        <  1:1612153/70‑1 (MQ=255)
  aaGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCAtt                                                                      >  1:2428842/1‑71 (MQ=255)
     gCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTg                                                                   <  1:5113514/71‑1 (MQ=255)
        aGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACGTGTCTCTATTCCGACATCAttt                                                                     >  1:4358453/1‑66 (MQ=255)
        aGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGcc                                                                 >  1:4173647/1‑70 (MQ=255)
         gCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGAcatca                                                                        >  1:110470/1‑62 (MQ=255)
         gCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGa                                                               >  1:5493622/1‑71 (MQ=255)
         gCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGa                                                               <  1:4925303/71‑1 (MQ=255)
            ggATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTACGAcatca                                                                        >  1:5185177/1‑59 (MQ=255)
             gATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           <  1:5279210/71‑1 (MQ=255)
             gATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           <  1:2478558/71‑1 (MQ=255)
              aTCTGGAGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           >  1:728416/1‑70 (MQ=255)
                   gtggtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGActt                                                      <  1:3872112/70‑3 (MQ=255)
                      gtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCAtt                                                                      <  1:3865070/51‑1 (MQ=255)
                      gtTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCAtt                                                                      <  1:983705/51‑1 (MQ=255)
                       gtACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGcc                                                                 <  1:3076230/54‑1 (MQ=255)
                         aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACg                                                <  1:2530617/70‑1 (MQ=255)
                         aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACg                                                <  1:4562829/70‑1 (MQ=255)
                         aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACg                                                >  1:2414707/1‑70 (MQ=255)
                         aCGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACg                                                <  1:1473821/70‑1 (MQ=255)
                          cGCTCGACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaa                                              <  1:774887/71‑1 (MQ=255)
                           gCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaa                                             <  1:5376024/71‑1 (MQ=255)
                           gCTCGACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaa                                             <  1:3798898/71‑1 (MQ=255)
                             tcgACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaaa                                            >  1:1865983/3‑70 (MQ=255)
                              cgACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaa                                              >  1:2054885/2‑67 (MQ=255)
                               gACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaaa                                           <  1:227333/69‑1 (MQ=255)
                               gACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaaa                                           <  1:2869982/69‑1 (MQ=255)
                               gACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGaaaaa                                           <  1:2516655/69‑1 (MQ=255)
                               gACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAga                                         >  1:3497426/1‑71 (MQ=255)
                               gACTTCCGCATGTCCAGTACCTGCCTGTTCTCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAga                                         >  1:3490634/1‑71 (MQ=255)
                                aCTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGcc                                                                 >  1:3902865/1‑46 (MQ=255)
                                  ttCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAgacga                                      >  1:2829301/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGAc                                                        >  1:4541119/1‑51 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:3333857/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:5451873/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:3799207/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:1729023/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:3290762/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:252478/1‑71 (MQ=255)
                                    ccGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGCCGACCTGGTACGAAAAAGACGACa                                    >  1:3451766/1‑71 (MQ=255)
                                    ccGTCTCTCGAGCACCTGTCTCTATTCCGAcatca                                                                        >  1:4583525/1‑35 (MQ=255)
                                     cGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaa                                             >  1:4675448/1‑61 (MQ=255)
                                     cGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:590478/1‑70 (MQ=255)
                                      gTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaag                                             >  1:5404182/1‑59 (MQ=255)
                                      gTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaa                                            >  1:1978027/1‑61 (MQ=255)
                                           tCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGAc                                                        >  1:2661012/1‑44 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           <  1:990790/39‑1 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           <  1:3008983/39‑1 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGc                                                           <  1:4672097/39‑1 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:460371/1‑62 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:2271004/1‑62 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:4517095/1‑62 (MQ=255)
                                             gAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACa                                    >  1:3676956/1‑62 (MQ=255)
                                              aGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTc                          >  1:5319269/1‑71 (MQ=255)
                                               gCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCg                         >  1:2561185/1‑71 (MQ=255)
                                                    tGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaaaa                                           <  1:5502763/48‑1 (MQ=255)
                                                     gTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATg                   >  1:5295264/1‑71 (MQ=255)
                                                      tctcTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGaaa                                             <  1:4890858/44‑1 (MQ=255)
                                                      tctcTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATAc                             >  1:4163088/1‑60 (MQ=255)
                                                      tctcTATTCCGACATCATTTTGCCGACCGCGACCTg                                                     >  1:2024091/1‑36 (MQ=255)
                                                          tATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCa                 <  1:2424132/68‑1 (MQ=255)
                                                          tATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATcc              >  1:2999031/1‑71 (MQ=255)
                                                            ttCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCg             <  1:3539171/70‑1 (MQ=255)
                                                            ctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAg                                          <  1:541957/40‑1 (MQ=12)
                                                            ctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGaa                                >  1:1923086/2‑51 (MQ=255)
                                                            ctCCGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGt            >  1:141150/2‑71 (MQ=255)
                                                             tCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGc                  >  1:3065344/1‑64 (MQ=255)
                                                             tCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGc                  >  1:983598/1‑64 (MQ=255)
                                                              ccGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAgac                                        >  1:3400195/1‑41 (MQ=16)
                                                              ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa                                >  1:1487850/1‑49 (MQ=255)
                                                              ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGaa                                >  1:2381677/1‑49 (MQ=255)
                                                              ccGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGtt           <  1:5072479/70‑1 (MQ=255)
                                                               cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAgac                                        <  1:384137/40‑1 (MQ=16)
                                                               cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAgac                                        <  1:416510/40‑1 (MQ=16)
                                                               cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATg                                  <  1:4124788/46‑1 (MQ=255)
                                                               cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa         >  1:2054840/1‑71 (MQ=255)
                                                               cGATATCGTTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa         >  1:4247396/1‑71 (MQ=255)
                                                               cGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTa         >  1:2743258/1‑71 (MQ=255)
                                                                gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTa         <  1:1043388/67‑1 (MQ=255)
                                                                gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt        >  1:892632/4‑71 (MQ=255)
                                                                gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt        >  1:892630/4‑71 (MQ=255)
                                                                gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt        >  1:3897985/4‑71 (MQ=255)
                                                                gatatcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGATATGCATCCGTTTAt        >  1:3568848/4‑71 (MQ=255)
                                                                 aCATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATa                              >  1:1793678/1‑48 (MQ=255)
                                                                 aCATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTa         >  1:426848/1‑69 (MQ=255)
                                                                  catcatTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTc      <  1:5664120/71‑1 (MQ=255)
                                                                   atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGata                     >  1:3466423/1‑55 (MQ=255)
                                                                   atcgtTCTGCCCACCGCCACCTGGTACGAAAAAGACGATATGAACACCTCGGata                     >  1:4274569/1‑55 (MQ=255)
                                                                   atcgtTCTGCCCACCGCCACCTGCTACGAAAAAGACGATATGaa                                >  1:4673438/1‑44 (MQ=12)
                                                                    tcatTTTGCCGACGGCGACCTGGTACGAAAAAgac                                        <  1:1829124/35‑1 (MQ=255)
                                                                     catTTTGCCGACGGCGACCTGGTACGAAAAAGAAGACATGAATACTTCGGATATGCATCCGTTTATTCAcc   >  1:2473935/1‑71 (MQ=255)
                                                                      atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCg                         <  1:1370847/48‑1 (MQ=255)
                                                                      atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGa                       <  1:4351762/50‑1 (MQ=255)
                                                                      atTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCAccc  >  1:1279436/1‑71 (MQ=255)
                                                                      |                                                                      
GGAAGGCAAGCTGGATCTGGTGGTTACGCTGGACTTCCGTCTGTCGAGCACCTGTCTCTATTCCGACATCATTTTGCCGACGGCGACCTGGTACGAAAAAGACGACATGAATACTTCGGATATGCATCCGTTTATTCACCC  >  minE/833828‑833968

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