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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,657,322 T→C 72.0% S531S (AGT→AGC)  ppk → polyphosphate kinase, component of RNA degradosome

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,657,3220TC72.0% 105.4 / 39.5 96S531S (AGT→AGC) ppkpolyphosphate kinase, component of RNA degradosome
Reads supporting (aligned to +/- strand):  ref base T (9/18);  new base C (36/33);  total (45/51)
Fisher's exact test for biased strand distribution p-value = 1.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

CTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGT  >  minE/1657256‑1657377
                                                                  |                                                       
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:2299615/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:785441/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:3039124/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:3209531/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:1572911/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       >  1:1410758/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg                                                       <  1:713941/69‑1 (MQ=255)
 tCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGt                                                      <  1:1402753/69‑1 (MQ=255)
     gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa                                                  <  1:825714/69‑1 (MQ=255)
     gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa                                                  <  1:2621787/69‑1 (MQ=255)
     gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa                                                  <  1:2577504/69‑1 (MQ=255)
     gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa                                                  <  1:1664296/69‑1 (MQ=255)
     gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa                                                  <  1:1026363/69‑1 (MQ=255)
               gTATGAAATGGTGGACCGCGAGATAGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGc                                         >  1:2675420/1‑68 (MQ=255)
               gTATGAAATGGTGGAC‑‑CGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTa                                       >  1:1619275/1‑68 (MQ=255)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCTGTATCACCCTGAAGCTAAAt                                    <  1:1297991/59‑1 (MQ=38)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCTGTATCACCCTGAAGCTAAAt                                    <  1:1938562/59‑1 (MQ=38)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:2112694/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:2220352/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:199335/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:2293788/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:3394529/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:844739/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:2453252/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:3091592/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:647412/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:3085999/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:1130276/59‑1 (MQ=39)
                             aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:516596/59‑1 (MQ=39)
                              ccGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGa                         <  1:1982773/69‑1 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:300742/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:624458/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:1799385/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:3430817/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:367593/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:593911/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:40419/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:464025/1‑69 (MQ=255)
                                 cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa                      >  1:1288114/1‑69 (MQ=255)
                                     aTCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGc                  <  1:1901476/69‑1 (MQ=255)
                                     aTCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGc                  <  1:1854658/69‑1 (MQ=255)
                                     aTCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGc                  <  1:1737815/69‑1 (MQ=255)
                                     aTCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGc                  <  1:388228/69‑1 (MQ=255)
                                      tCGCCAAGGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:638482/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1044592/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:3424151/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:515427/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:478565/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:3092253/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:380156/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:3195569/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:3234189/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2168108/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1129104/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:874986/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1382249/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1400575/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1429378/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1581062/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:1703267/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2071431/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2453728/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2480560/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:715780/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2733317/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2831448/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2928641/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2978043/1‑52 (MQ=255)
                                      tCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCAGAAGCTAAATaa                                  >  1:691821/1‑52 (MQ=39)
                                      tCGACAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATaa                                  >  1:2230973/1‑52 (MQ=255)
                                          cAACGCGCAGCAATGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:1286744/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGTTATCACCCTGAAGCTAAAt                                    <  1:1613983/46‑1 (MQ=39)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGTAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:3148114/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:586514/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:971400/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:836537/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:646465/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:528032/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:1327185/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:502627/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:3424195/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:3265788/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:2976667/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:2632953/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:2519973/69‑1 (MQ=255)
                                          cAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:2308612/69‑1 (MQ=255)
                                           aaCGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGt             <  1:2803410/68‑1 (MQ=255)
                                                 cagcaAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGc                  <  1:744915/57‑1 (MQ=255)
                                                   gcaAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt                                    <  1:2225201/37‑1 (MQ=255)
                                                    caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg   <  1:701799/69‑1 (MQ=255)
                                                    caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg   <  1:1961646/69‑1 (MQ=255)
                                                    caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg   <  1:548816/69‑1 (MQ=255)
                                                    caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg   <  1:2699902/69‑1 (MQ=255)
                                                    caAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTg   <  1:586830/69‑1 (MQ=255)
                                                     aaGGGCTGCCCAGCGGTATCACACTGAAGCTAAAt                                    <  1:1078061/35‑1 (MQ=255)
                                                      aGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGt  >  1:1753866/1‑68 (MQ=255)
                                                                  |                                                       
CTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAAAGGCCTGGTTGATCGTCTGT  >  minE/1657256‑1657377

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