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 2,572,736 T→A 25.0% intergenic (+1504/‑275) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7360TA25.0% 106.0 / 41.3 64intergenic (+1504/‑275)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (29/19);  new base A (13/3);  total (42/22)
Fisher's exact test for biased strand distribution p-value = 2.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.30e-01

CCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTA  >  minE/2572667‑2572806
                                                                     |                                                                      
ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                        >  1:2295665/1‑70 (MQ=255)
   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                        <  1:1563705/67‑1 (MQ=255)
     aaccGGATTCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATAcc                                                                  >  1:3568319/4‑71 (MQ=255)
     aaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAcc                                                                  >  1:347736/1‑71 (MQ=255)
         ggattCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGccc                                                              >  1:1572421/4‑71 (MQ=255)
          ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGtt                                                                       >  1:779276/1‑61 (MQ=255)
          gattCAGCGGATACGCATACAGACTCCATCCCCCCACCAGCCCTATCGGGTCCTGAGTGATATACCGcccc                                                             >  1:1313014/3‑71 (MQ=255)
           attCAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCct                                                            <  1:590119/70‑1 (MQ=255)
               agcGGATACGCATACAGACTCCATCCCCCCTCCAGCCCTATCGGGTCCTGAGTGATATACCGCCCctgca                                                         <  1:2009461/68‑2 (MQ=255)
                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                                                       >  1:1705092/1‑71 (MQ=255)
                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCtgcagc                                                       >  1:3842904/1‑71 (MQ=255)
                aCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                       >  1:1264693/1‑71 (MQ=255)
                 cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                                                      >  1:971589/1‑71 (MQ=255)
                  ggATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCgg                                                     >  1:3260527/1‑71 (MQ=255)
                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTTTTATACCGCCCCTGCTGCGGt                                                    <  1:2939456/71‑1 (MQ=255)
                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                                                    <  1:3895595/71‑1 (MQ=255)
                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                                                    <  1:858554/71‑1 (MQ=255)
                    aTACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgggt                                                   >  1:2302654/1‑69 (MQ=255)
                    aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCgg                                                     >  1:95052/1‑69 (MQ=255)
                     tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTa                                                  <  1:1229746/71‑1 (MQ=255)
                      aCTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                        <  1:558483/48‑1 (MQ=255)
                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGAtata                                                                    >  1:2244817/1‑50 (MQ=255)
                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATAc                                                                   >  1:609916/1‑51 (MQ=255)
                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctgc                                                          <  1:1437110/60‑1 (MQ=255)
                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGtt                                                                       >  1:1270654/1‑47 (MQ=255)
                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                      >  1:230084/1‑48 (MQ=255)
                        tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                      >  1:2116853/1‑48 (MQ=255)
                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                             <  1:420021/71‑1 (MQ=255)
                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                             <  1:2991903/71‑1 (MQ=255)
                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGt                                              <  1:2367022/70‑1 (MQ=255)
                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGt                                              >  1:1480502/1‑70 (MQ=255)
                           tAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGAta                                                                      >  1:1796954/1‑44 (MQ=255)
                            aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAAt                                                >  1:1951617/1‑66 (MQ=255)
                            aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAc                                           >  1:18002/1‑71 (MQ=255)
                              aaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAcc                                          >  1:1885943/1‑70 (MQ=255)
                                aTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGa                                        >  1:1505057/1‑70 (MQ=255)
                                 ttCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgctg                                                        <  1:2546707/53‑1 (MQ=255)
                                   ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                             >  1:462565/1‑62 (MQ=255)
                                   ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                             >  1:3575229/1‑62 (MQ=255)
                                     acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg                                  <  1:1701539/71‑1 (MQ=255)
                                        tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt                                 >  1:1640274/1‑69 (MQ=255)
                                         acctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGtt                                                   >  1:3536187/1‑50 (MQ=255)
                                         acctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                               >  1:1234728/1‑70 (MQ=255)
                                          cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                               >  1:3408042/1‑69 (MQ=255)
                                           ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                            >  1:33221/1‑71 (MQ=255)
                                              ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTa                                            >  1:2369483/1‑52 (MQ=255)
                                              ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                          >  1:2098054/1‑70 (MQ=255)
                                               cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                          >  1:2448899/1‑69 (MQ=255)
                                                  cccAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAAt                                                >  1:3901818/1‑44 (MQ=255)
                                                  cccAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGcc                     >  1:1589666/1‑71 (MQ=255)
                                                  cccAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGcc                     <  1:2415230/71‑1 (MQ=255)
                                                     aaTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGcg                     >  1:438408/1‑67 (MQ=255)
                                                     aaTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                   >  1:1836065/1‑70 (MQ=255)
                                                         ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt               <  1:1580718/70‑1 (MQ=255)
                                                         ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt               <  1:872306/70‑1 (MQ=255)
                                                         ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt               <  1:2982393/70‑1 (MQ=255)
                                                           atccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAGCGataa                                     <  1:654806/44‑1 (MQ=255)
                                                           aGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGtt                                <  1:3340648/51‑1 (MQ=255)
                                                           aGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcat            >  1:1845928/1‑71 (MQ=255)
                                                             ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcat            <  1:2594785/69‑1 (MQ=255)
                                                             ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcat            <  1:2599422/69‑1 (MQ=255)
                                                              cTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat         <  1:2546252/71‑1 (MQ=255)
                                                              cTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat         >  1:2800266/1‑71 (MQ=255)
                                                              cTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat         >  1:2757228/1‑71 (MQ=255)
                                                               tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACa                        >  1:699314/1‑55 (MQ=255)
                                                               tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACa                        >  1:1807583/1‑55 (MQ=255)
                                                                 aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatca       >  1:3186258/1‑70 (MQ=255)
                                                                 aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcatc        <  1:252641/69‑1 (MQ=255)
                                                                 aGTGTTATACCGCCCCTGCTGCGCTTAATGTTACCGATAATAGTTATAGTACAGCCCTGa                 >  1:228955/1‑60 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTAc                         <  1:3376186/48‑1 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCAtacta  >  1:2032810/1‑71 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCAtact   <  1:185563/70‑1 (MQ=255)
                                                                     |                                                                      
CCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACTA  >  minE/2572667‑2572806

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