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 1,502,353 G→A 71.4% S92L (TCA→TTA)  lrhA ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,502,3530GA71.4% 100.0 / 53.0 77S92L (TCA→TTA) lrhADNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base G (10/12);  new base A (23/32);  total (33/44)
Fisher's exact test for biased strand distribution p-value = 8.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.92e-01

GGTAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGCCATGTT  >  minE/1502284‑1502422
                                                                     |                                                                     
ggTAAGATCGTATCGGCAGATTCATCTGAAGCAACGATAGTTAATACGCCCTGAAGATTACTGAACATtga                                                                      <  1:2239079/71‑1 (MQ=255)
 gTAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:2825380/71‑1 (MQ=255)
 gTAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:4962868/71‑1 (MQ=255)
   aaGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatga                                                                   >  1:4263170/1‑71 (MQ=255)
   aaGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatg                                                                    <  1:2891828/70‑1 (MQ=255)
    aGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtgatgat                                                                  >  1:1772087/1‑71 (MQ=255)
    aGATCGTATCGGCAGATTCATCTGAAGAACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatgat                                                                  <  1:2336477/71‑1 (MQ=255)
       tCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAg                                                               <  1:4113028/71‑1 (MQ=255)
       tCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAg                                                               <  1:5419225/71‑1 (MQ=255)
              ggCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatgatga                                                                <  1:1108886/63‑1 (MQ=255)
                 aGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAg                                                               <  1:5216287/61‑1 (MQ=255)
                 aGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtcat                                                     <  1:2177312/71‑1 (MQ=255)
                 aGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcat                                                     >  1:3739483/1‑71 (MQ=255)
                   aTTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcatca                                                   >  1:2695602/1‑71 (MQ=255)
                    ttCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCtcat                                                     >  1:1285252/1‑68 (MQ=255)
                    ttCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAg                                                               <  1:913042/58‑1 (MQ=255)
                    ttCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTcatcat                                                  <  1:1541455/71‑1 (MQ=255)
                      cATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCa                                                             >  1:1688282/1‑58 (MQ=255)
                       aTCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaa                                               <  1:4456012/71‑1 (MQ=255)
                       aTCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaa                                               <  1:5603238/71‑1 (MQ=255)
                         cTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaaa                                              >  1:2275021/1‑70 (MQ=255)
                           gAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACg                                           >  1:4304129/1‑71 (MQ=255)
                            aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACg                                           <  1:101116/70‑1 (MQ=255)
                            aaGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGc                                          <  1:2606949/71‑1 (MQ=255)
                             aGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGc                                          <  1:4267768/70‑1 (MQ=255)
                              gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatg                                                                    <  1:1739875/43‑1 (MQ=255)
                              gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATtaatg                                                                    <  1:5574860/43‑1 (MQ=255)
                              gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAg                                        <  1:3999934/71‑1 (MQ=255)
                              gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAg                                        <  1:2248706/71‑1 (MQ=255)
                              gCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAg                                        <  1:1399680/71‑1 (MQ=255)
                                 ccGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:2176617/39‑1 (MQ=255)
                                 ccGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:4310066/39‑1 (MQ=255)
                                 ccGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:3421265/39‑1 (MQ=255)
                                 ccGATAGTTAATACGCCCTGAAGATTACTGAACATtaat                                                                     <  1:2385389/39‑1 (MQ=255)
                                 ccGATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAt                                     >  1:1851056/1‑71 (MQ=255)
                                   gATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                   >  1:611902/1‑71 (MQ=255)
                                   gATAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                   >  1:1075667/1‑71 (MQ=255)
                                    aTAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTaaaa                                             >  1:4494701/1‑60 (MQ=255)
                                     tAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:3549175/71‑1 (MQ=255)
                                     tAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:1450404/71‑1 (MQ=255)
                                     tAGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:2413594/71‑1 (MQ=255)
                                     caGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:5470292/70‑1 (MQ=255)
                                      aGTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTcc                                >  1:4058042/1‑71 (MQ=255)
                                       gTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCt                               >  1:4879952/1‑71 (MQ=255)
                                       gTTAATACGCCCTGAAGATTACTGAACATTAATGATGAg                                                               <  1:5471502/39‑1 (MQ=255)
                                       gTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                   <  1:177308/67‑1 (MQ=255)
                                       gTTAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:220712/69‑1 (MQ=255)
                                        ttAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACg                                           <  1:4429584/58‑1 (MQ=255)
                                        ttAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTg                              <  1:2008972/71‑1 (MQ=255)
                                         tAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTgg                             >  1:4727244/1‑71 (MQ=255)
                                         tAATACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 >  1:3737608/1‑67 (MQ=255)
                                          aaTACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaaaa                                             >  1:1750752/1‑54 (MQ=255)
                                          aaTACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGc                            >  1:5436085/1‑71 (MQ=255)
                                           aTACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGc                            <  1:1560820/70‑1 (MQ=255)
                                            tccGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                          <  1:5568086/69‑1 (MQ=255)
                                            tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGc                            >  1:3688278/1‑69 (MQ=255)
                                            tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                          <  1:4783014/71‑1 (MQ=255)
                                            tACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                          <  1:4294762/71‑1 (MQ=255)
                                            tACGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                          <  1:5537475/71‑1 (MQ=255)
                                              cGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcat                                                     >  1:2543261/1‑42 (MQ=255)
                                              cGCCCTGAAGATTACTGAACATTAATGATGAGCAGGCCtcat                                                     >  1:1873940/1‑42 (MQ=255)
                                                cccTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAAcc                      <  1:4670237/71‑1 (MQ=255)
                                                cccTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAAc                       >  1:1163387/1‑70 (MQ=255)
                                                 ccTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCa                     <  1:2595546/71‑1 (MQ=255)
                                                  cTGAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa                    <  1:3256079/71‑1 (MQ=255)
                                                   tGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 >  1:3805042/1‑57 (MQ=255)
                                                   tGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTc                                 <  1:3437739/57‑1 (MQ=255)
                                                    gAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:1582250/1‑70 (MQ=255)
                                                    gAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:4151803/1‑70 (MQ=255)
                                                    gAAGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:5184145/1‑70 (MQ=255)
                                                     aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:5235232/1‑69 (MQ=255)
                                                     aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   <  1:5463919/69‑1 (MQ=255)
                                                     aaGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaa                    >  1:5633392/1‑68 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGTCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   <  1:3271006/69‑1 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTaaaa                                             >  1:1096558/1‑43 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:1960009/1‑69 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   >  1:2812461/1‑69 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   <  1:23455/69‑1 (MQ=255)
                                                     aaGATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaag                   <  1:230341/69‑1 (MQ=255)
                                                       gATTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGt               >  1:363608/1‑71 (MQ=255)
                                                        aTTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTg                              <  1:1662675/55‑1 (MQ=255)
                                                        aTTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTg                              <  1:1118888/55‑1 (MQ=255)
                                                        aTTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGt                          <  1:699055/59‑1 (MQ=255)
                                                        aTTACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGtt              <  1:1987069/71‑1 (MQ=255)
                                                         ttACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg             <  1:3307326/71‑1 (MQ=255)
                                                          tACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGc                            >  1:2519391/1‑55 (MQ=255)
                                                          tACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCaagaa                 >  1:371009/1‑66 (MQ=255)
                                                          tACTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTaa                        >  1:2747789/1‑59 (MQ=255)
                                                           aCTGAACATTAATGATGAGCAGGCCTCATCATTAAAACGCAGGAttt                                   <  1:3884267/47‑1 (MQ=255)
                                                                  aTTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg             <  1:4127021/62‑1 (MQ=255)
                                                                  aTTAATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTg             <  1:2687156/62‑1 (MQ=255)
                                                                    tgatgatgaGCAGGCCTCATCATTAAAACGCAGGATTTTTCTGGCGTAACCAAGAAGTTGAATGCCATGtt  >  1:571877/1‑71 (MQ=255)
                                                                     |                                                                     
GGTAAGATCGTATCGGCAGATTCATCTGAAGCACCGATAGTTAATACGCCCTGAAGATTACTGAACATTGATGATGAGCAGGCCTCATCATTAAAACGCAGGATTTTCCTGGCGTAACCAAGAAGTTGAATGCCATGTT  >  minE/1502284‑1502422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A