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 423,971 T→C 21.7% S309G (AGT→GGT)  nagC ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE423,9710TC21.7% 113.2 / 28.6 60S309G (AGT→GGT) nagCDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (7/6);  total (31/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TTGATAGCAATGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCACGCGGCTCTGG  >  minE/423904‑424038
                                                                   |                                                                   
ttGATAGCAATGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATc                                                                  >  1:433765/1‑71 (MQ=255)
   aTAGCAATGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGc                                                                <  1:2279430/70‑1 (MQ=255)
    tAGCAATGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACCATCGCCt                                                              <  1:1630812/71‑1 (MQ=255)
         aTGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGt                                                          <  1:2019439/70‑1 (MQ=255)
          tGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTc                                                        >  1:2472195/1‑71 (MQ=255)
           ggCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTcg                                                       >  1:2412007/1‑71 (MQ=255)
           ggCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTcg                                                       >  1:1834528/1‑71 (MQ=255)
            gCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTcgc                                                      >  1:2469192/1‑71 (MQ=255)
             cGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTcgcg                                                     >  1:1804353/1‑71 (MQ=255)
              gATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCgg                                                    <  1:213685/71‑1 (MQ=255)
                  gTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTg                                                           <  1:768270/60‑1 (MQ=255)
                  gTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTg                                                           <  1:763649/60‑1 (MQ=255)
                   ttttACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTg                                               >  1:3603038/1‑71 (MQ=255)
                   ttttACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTc                                                        <  1:2768108/62‑1 (MQ=255)
                    tttACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGtt                                                         >  1:1496182/1‑60 (MQ=255)
                      tACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCa                                             <  1:3760757/70‑1 (MQ=255)
                      tACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGc                                              >  1:1196525/1‑69 (MQ=255)
                       aCCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAg                                            <  1:3334144/70‑1 (MQ=255)
                         cctgATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAg                                            <  1:527711/65‑1 (MQ=255)
                           aGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGt                                       >  1:3287182/1‑71 (MQ=255)
                            gATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGtt                                      >  1:3329528/1‑71 (MQ=255)
                              tGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGa                                           >  1:845777/1‑64 (MQ=255)
                              tGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGa                                           >  1:841139/1‑64 (MQ=255)
                                  gaccgacATACTCAATTACTTCCGACGCCAGACTATCGcc                                                               <  1:152755/40‑1 (MQ=255)
                                   accgacATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATgg                               >  1:189144/1‑71 (MQ=255)
                                     cgacATACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTg                             <  1:2557853/71‑1 (MQ=255)
                                      gacATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCtt                                                 <  1:3171320/50‑1 (MQ=255)
                                      gacATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGtttt                                    <  1:1866886/63‑1 (MQ=255)
                                        cATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGa                                  >  1:65431/1‑63 (MQ=255)
                                        cATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGa                                  >  1:1286508/1‑63 (MQ=255)
                                         aTACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgt                         >  1:2998021/1‑71 (MQ=255)
                                         aTACTCAATTACTTCCGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgt                         >  1:2423606/1‑71 (MQ=255)
                                          tACTCAATTACTTCCGACGCCAGACTATCGCCTTTg                                                           <  1:1146597/36‑1 (MQ=255)
                                          tACTCAATTACTTCCGACGCCAGACTATCGCCTTTg                                                           <  1:2873527/36‑1 (MQ=255)
                                            cTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgtcgt                      >  1:1072843/1‑71 (MQ=255)
                                               aaTTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgtcgtc                     <  1:981787/69‑1 (MQ=255)
                                               aaTTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgtcgtc                     <  1:3374289/69‑1 (MQ=255)
                                               aaTTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTcc                    <  1:2575503/70‑1 (MQ=255)
                                                aTTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCa                   <  1:825568/70‑1 (MQ=255)
                                                 ttACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAg                  >  1:1744229/1‑70 (MQ=255)
                                                 ttACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGc                 >  1:86332/1‑71 (MQ=255)
                                                 ttACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGc                 >  1:3283930/1‑71 (MQ=255)
                                                   aCTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCg                <  1:2095931/70‑1 (MQ=255)
                                                   aCTTCCGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCgg               >  1:3931347/1‑71 (MQ=255)
                                                    cTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgtc                        <  1:290946/61‑1 (MQ=255)
                                                     ttCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGtttt                                    <  1:2387608/48‑1 (MQ=255)
                                                       ccGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCa             <  1:3037011/69‑1 (MQ=255)
                                                       ccGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCAcg           >  1:1815423/1‑71 (MQ=255)
                                                       ccGACGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCAc            <  1:462742/70‑1 (MQ=255)
                                                        cGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCAcg           >  1:1582954/1‑70 (MQ=255)
                                                          aCGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGa                                  >  1:2753791/1‑45 (MQ=255)
                                                          aCGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCACGCgg        >  1:2280363/1‑71 (MQ=255)
                                                          aCGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGAt                                          <  1:3776582/37‑1 (MQ=255)
                                                          aCGCCAGACCATCGCCTTTGTTCGCGGCTTTGCAGAt                                          <  1:2056184/37‑1 (MQ=255)
                                                              cAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAg                          >  1:641527/1‑49 (MQ=255)
                                                                gACTATCGCCTTTGTTCGCGGCTTTGCAGATAGtttt                                    <  1:509221/37‑1 (MQ=255)
                                                                gACTATCGCCTTTGTTCGCGGCTTTGCAGATAGtttt                                    <  1:3083784/37‑1 (MQ=255)
                                                                gACCATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAgtcgt                      >  1:1363561/1‑51 (MQ=255)
                                                                 aCTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCACGCGGCTCTgg  >  1:2612048/1‑70 (MQ=255)
                                                                  cTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCACGCGGCTCTgg  >  1:3686377/1‑69 (MQ=255)
                                                                   |                                                                   
TTGATAGCAATGGCGATGGTTTTACCCAGATGACGACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATGGTGCAGTCGTCCAGCGGCACGCGGCTCTGG  >  minE/423904‑424038

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