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 2,627,458 C→T 30.6% intergenic (+198/‑73) rpoH → / → livJ RNA polymerase, sigma 32 (sigma H) factor/leucine/isoleucine/valine transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,627,4580CT30.6% 126.5 / 62.4 130intergenic (+198/‑73)rpoH/livJRNA polymerase, sigma 32 (sigma H) factor/leucine/isoleucine/valine transporter subunit
Reads supporting (aligned to +/- strand):  ref base C (53/37);  new base T (29/11);  total (82/48)
Fisher's exact test for biased strand distribution p-value = 1.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

Only 100 of 166 total aligned reads displayed.

CTATTCCAATATCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGATT  >  minE/2627391‑2627524
                                                                   |                                                                  
cTATTCCAATATCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGc                                                                    >  1:1281061/1‑68 (MQ=255)
cTATTCCAATATCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGc                                                                    >  1:1828418/1‑68 (MQ=255)
          atCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaa                                                          >  1:2876972/1‑68 (MQ=255)
          atCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaa                                                          >  1:1317310/1‑68 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:2919187/69‑1 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:2555497/69‑1 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:876819/69‑1 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:2713451/69‑1 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:86059/69‑1 (MQ=255)
           tCATAAAAATGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGCTACGTATAAAACGAAAt                                                        <  1:2287792/69‑1 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:1723230/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:3310123/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:3134148/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:1081325/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:2019809/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:2753797/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:2977360/1‑68 (MQ=255)
           tCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGaaa                                                         >  1:1107181/1‑68 (MQ=255)
                aaaaTGGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGt                                                   >  1:2676513/1‑69 (MQ=255)
                aaaaTCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGt                                                   >  1:600934/1‑69 (MQ=255)
                aaaaTCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGt                                                   >  1:1423567/1‑69 (MQ=255)
                aaaaTCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGt                                                   >  1:1920309/1‑69 (MQ=255)
                   aTCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGc                                                 >  1:2314334/1‑68 (MQ=255)
                   aTCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGc                                                 >  1:2934754/1‑68 (MQ=255)
                          aTGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaac                                         <  1:841115/69‑1 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:1991927/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:1124701/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:2862916/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:1253461/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:134756/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:3109676/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:2508800/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      <  1:2395650/69‑1 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      <  1:1717575/69‑1 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      >  1:538281/1‑69 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      <  1:1851147/69‑1 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaac                                      <  1:500255/69‑1 (MQ=255)
                             ttttAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAaacaa                                       <  1:424749/68‑1 (MQ=255)
                                    agagTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCacaa                               <  1:2214616/69‑1 (MQ=255)
                                    agagTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCacaa                               <  1:2450874/69‑1 (MQ=255)
                                    agagTATGCTGCTAAAGCACGGGTACTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCacaa                               <  1:792363/69‑1 (MQ=255)
                                        tATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacaca                           <  1:1172861/69‑1 (MQ=255)
                                        tATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacaca                           <  1:405143/69‑1 (MQ=255)
                                        tATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacaca                           <  1:538671/69‑1 (MQ=255)
                                        tATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacaca                           <  1:2481067/69‑1 (MQ=255)
                                        tATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacaca                           <  1:2966794/69‑1 (MQ=255)
                                          tgctgcTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacacac                          >  1:3033120/1‑68 (MQ=255)
                                          tgctgcTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacacac                          >  1:3022089/1‑68 (MQ=255)
                                          tgctgcTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacacac                          >  1:417262/1‑68 (MQ=255)
                                          tgctgcTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAacacac                          >  1:3399875/1‑68 (MQ=255)
                                            ctgctAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGt                        <  1:2604261/68‑1 (MQ=255)
                                            ctgctAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGt                        >  1:2834637/1‑68 (MQ=255)
                                            ctgctAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGt                        <  1:1831317/68‑1 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGGACAACAACATCACAacacac                          >  1:3160496/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACTTCACAacacac                          >  1:2554691/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAataca                           >  1:878634/1‑56 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:2659112/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:309436/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:550690/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:370838/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:3173566/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:327869/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:3354798/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:1343352/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:1499013/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:2539198/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:1687087/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:2428003/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:1777977/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacacac                          >  1:2225268/1‑57 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATCACAacaca                           >  1:2934237/1‑56 (MQ=255)
                                                     cACGGGTAGCTACGTATAAAACGAAATAAAGTGCTGCACAACAACATAACAacacac                          >  1:3193433/1‑57 (MQ=255)
                                                         ggTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAgaagaa          <  1:1119225/69‑1 (MQ=255)
                                                         ggTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAgaagaa          <  1:2593001/69‑1 (MQ=255)
                                                             gTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      >  1:2352766/1‑69 (MQ=255)
                                                               cATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGa    <  1:2774974/69‑1 (MQ=255)
                                                               cATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGa    <  1:1699310/69‑1 (MQ=255)
                                                               cATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGa    <  1:1902732/69‑1 (MQ=255)
                                                               cATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGa    <  1:2172956/69‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATca                                  >  1:1523486/1‑35 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGta                       >  1:2637923/1‑46 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:3364752/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      >  1:943018/1‑63 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:2688581/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:803014/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:1584043/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:741357/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:594508/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      >  1:2462366/1‑63 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:3257480/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:326157/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:2054670/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:2094616/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:2340374/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATggg      <  1:2305021/63‑1 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGAtt  >  1:1669350/1‑67 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGAtt  >  1:2364120/1‑67 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGAtt  >  1:84005/1‑67 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGAtt  >  1:846191/1‑67 (MQ=255)
                                                                   cATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGAtt  >  1:2665606/1‑67 (MQ=255)
                                                                   |                                                                  
CTATTCCAATATCATAAAAATCGGGTATGTTTTAGCAGAGTATGCTGCTAAAGCACGGGTAGTCATGCATAAAACGAAATAAAGTGCTGAAAAACAACATCACAACACACGTAATAACCAGAAGAATGGGGATT  >  minE/2627391‑2627524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A