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 2,171,234 A→G 45.1% Q475Q (CAA→CAG)  rpoN → RNA polymerase, sigma 54 (sigma N) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,171,2340AG45.1% 15.0 / 84.8 102Q475Q (CAA→CAG) rpoNRNA polymerase, sigma 54 (sigma N) factor
Reads supporting (aligned to +/- strand):  ref base A (42/14);  new base G (28/18);  total (70/32)
Fisher's exact test for biased strand distribution p-value = 1.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.54e-01

Only 100 of 114 total aligned reads displayed.

AAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAATAACGTCGAG  >  minE/2171187‑2171298
                                               |                                                                
aaGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATa                                              >  1:663722/1‑68 (MQ=255)
aaGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATa                                              >  1:2762658/1‑68 (MQ=255)
aaGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATa                                              >  1:706692/1‑68 (MQ=255)
aaGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACACAACCGATa                                              >  1:1203008/1‑68 (MQ=255)
    aCCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGaa                                         >  1:1173722/1‑69 (MQ=255)
    aCCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGaa                                         >  1:2758729/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2544202/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:185525/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:583841/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1972636/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2012456/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2176490/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:3243560/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:230969/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2539168/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1163976/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:3068545/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2752471/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:3047056/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:2894957/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:3022669/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1738322/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:636017/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:150269/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:11966/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1738138/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1306114/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:1681894/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGac                                      >  1:845128/1‑69 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:257394/68‑1 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:1511511/68‑1 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:1574019/68‑1 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:2196046/68‑1 (MQ=255)
       gagaGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:1741018/68‑1 (MQ=255)
        agagTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       <  1:1504767/67‑1 (MQ=255)
         gagTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGacac                                    <  1:3249647/69‑1 (MQ=255)
         gagTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGacac                                    <  1:3390683/69‑1 (MQ=255)
         gagTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGacac                                    <  1:418299/69‑1 (MQ=255)
         gagTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGacac                                    <  1:2858620/69‑1 (MQ=255)
          agTCTTTATCCATTCCGCCGTCAAACCAGTGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACt                                   <  1:2265950/69‑1 (MQ=255)
          agTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACt                                   <  1:2320580/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:2762960/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:3053294/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:1170153/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:1105869/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:260877/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:3184575/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:2590224/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:772757/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:3189018/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:696230/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:3279708/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:386323/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:1694463/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:191057/69‑1 (MQ=255)
                    cATTCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:516946/69‑1 (MQ=255)
                      ttCCGCCGTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:2969353/67‑1 (MQ=255)
                       tCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAAc                       >  1:3135648/1‑68 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAGCTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         <  1:3101636/65‑1 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       >  1:489996/1‑51 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       >  1:2719219/1‑51 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       >  1:2595414/1‑51 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       >  1:231823/1‑51 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGa                                       >  1:2109434/1‑51 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGc                               >  1:731032/1‑59 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:40074/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:869935/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:1875648/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:1911931/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:3433829/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCa                              >  1:34154/1‑60 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACAt                     >  1:722516/1‑69 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACAt                     >  1:2378715/1‑69 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACAt                     >  1:517195/1‑69 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACAt                     >  1:428377/1‑69 (MQ=255)
                        ccgccgTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACAt                     >  1:1899507/1‑69 (MQ=255)
                                  aCCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAAt           <  1:620959/69‑1 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:2756654/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:2132500/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:1312519/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:803697/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:1639599/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:672941/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:1792316/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:1947412/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:2789853/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:2076866/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCaa                        >  1:2370056/1‑49 (MQ=255)
                                         tAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCa                         >  1:2129978/1‑48 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGAGACTATGCAGCTCAACATTACCGGa              >  1:1781672/1‑57 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAAc                       >  1:1551357/1‑48 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACa                      >  1:2237792/1‑49 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCgg               >  1:3403818/1‑56 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGa              >  1:567528/1‑57 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGa              >  1:2538883/1‑57 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGa              >  1:1539287/1‑57 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGa              >  1:3268219/1‑57 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAATAACg       >  1:3434925/1‑64 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAATAACGTCgag  <  1:3132006/69‑1 (MQ=255)
                                           aacaacTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAATAACGTCgag  <  1:3125385/69‑1 (MQ=255)
                                               |                                                                
AAGTACCGAGAGTCTTTATCCATTCCGCCGTCAAACCAGCGTAAACAACTCGTTTGACCCAACCGATAAGGAAGACACTATGCAGCTCAACATTACCGGAAATAACGTCGAG  >  minE/2171187‑2171298

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