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 2,572,736 T→A 40.6% 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
*minE2,572,7360TA40.6% 88.4 / 164.8 138intergenic (+1504/‑275)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (44/38);  new base A (38/18);  total (82/56)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

Only 100 of 161 total aligned reads displayed.

CCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACT  >  minE/2572667‑2572805
                                                                     |                                                                     
ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                       <  1:4341378/70‑1 (MQ=255)
ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                       <  1:1882051/70‑1 (MQ=255)
 cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     >  1:28989/1‑71 (MQ=255)
 cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     <  1:2017498/71‑1 (MQ=255)
   gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                                                    <  1:3519381/67‑1 (MQ=255)
   gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                                                    <  1:1170903/67‑1 (MQ=255)
   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTtata                                                                   <  1:1731037/71‑1 (MQ=255)
    agaTCGGATTCAACGGATACTGATAAAAATTCCATCCTCCTTTCAGCCCAATCGGATCCTGAGTGAtata                                                                   >  1:4143937/3‑70 (MQ=255)
       ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                                               >  1:1231848/2‑71 (MQ=255)
       ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                                               >  1:1660448/2‑71 (MQ=255)
          ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGcccc                                                            <  1:2673676/71‑1 (MQ=255)
            ttCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctg                                                          >  1:4336450/1‑71 (MQ=255)
            ttCAACGTATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     >  1:2577749/1‑60 (MQ=255)
            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     <  1:1139060/60‑1 (MQ=255)
            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     >  1:2413257/1‑60 (MQ=255)
            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     <  1:4411233/60‑1 (MQ=255)
             tCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCctg                                                          >  1:27694/1‑70 (MQ=255)
             tCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCct                                                           >  1:4019555/1‑69 (MQ=255)
              cAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCctgc                                                         <  1:5249456/70‑1 (MQ=255)
              cAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGccccag                                                          >  1:3173499/1‑67 (MQ=255)
              cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                                                     >  1:1947126/1‑58 (MQ=255)
              aaaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                       >  1:711242/2‑56 (MQ=255)
               aaCGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCctgcaa                                                       >  1:5397850/1‑69 (MQ=255)
               aaCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCctgcag                                                       >  1:1521892/1‑69 (MQ=255)
               aaCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCctgcag                                                       <  1:2167400/71‑3 (MQ=255)
               aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgctg                                                       >  1:3513883/1‑71 (MQ=255)
                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                                                       >  1:554642/1‑68 (MQ=255)
                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                                                       >  1:3815513/1‑68 (MQ=255)
                aCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:610003/1‑59 (MQ=255)
                 cGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCg                                                     <  1:4503678/71‑1 (MQ=255)
                  ggATACTGATAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGATATACCTCCCCTGCAGCggg                                                   >  1:2878568/1‑70 (MQ=255)
                  ggATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                                                    >  1:5171066/1‑71 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                       <  1:241324/52‑1 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                                       <  1:1911403/52‑1 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:1156018/1‑57 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:3432235/1‑57 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:5633958/1‑57 (MQ=255)
                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:666565/1‑57 (MQ=255)
                   gATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGccc                                                             <  1:175360/61‑1 (MQ=255)
                   gATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGAta                                                                     >  1:2706125/1‑53 (MQ=255)
                     tACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                                                       <  1:329436/65‑3 (MQ=255)
                         gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                                                    >  1:4979797/1‑64 (MQ=255)
                          aTAAAAATTCCATCCCGCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                                                  >  1:3379299/1‑48 (MQ=255)
                          aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                                                  >  1:1130632/1‑48 (MQ=255)
                          aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtata                                                                   >  1:3729263/1‑48 (MQ=255)
                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                                                  >  1:4383217/1‑49 (MQ=255)
                           tAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                                                      <  1:1807372/60‑1 (MQ=255)
                            aaaaaTTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGatat                                                                    >  1:4746828/1‑45 (MQ=255)
                                    cACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataat                                   <  1:967637/70‑1 (MQ=255)
                                     acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                      <  1:309814/50‑1 (MQ=255)
                                       ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                                                      <  1:399991/48‑1 (MQ=255)
                                       ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCgg                                                    >  1:2143794/1‑50 (MQ=255)
                                       ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCg                                                     >  1:2150441/1‑49 (MQ=255)
                                       ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt                                >  1:2631853/1‑70 (MQ=255)
                                        tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                                         <  1:3548074/44‑1 (MQ=255)
                                        tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                                         <  1:5145287/44‑1 (MQ=255)
                                        tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                                         <  1:158107/44‑1 (MQ=255)
                                         acctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta                              >  1:2439551/1‑70 (MQ=255)
                                           ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                           >  1:1943673/1‑71 (MQ=255)
                                           ctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                           <  1:5513053/71‑1 (MQ=255)
                                            ttCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTa                                           >  1:815782/1‑54 (MQ=255)
                                             tCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg                           >  1:1695969/1‑69 (MQ=255)
                                              tcAGCCCAATCGGATCCTGAGTGATATACCGcccc                                                            <  1:1132602/34‑1 (MQ=37)
                                              tcAGCCCAATCGGATCCTGAGTGATATACCGcccc                                                            <  1:4242852/34‑1 (MQ=37)
                                              ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                                         >  1:274979/1‑38 (MQ=255)
                                              ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                         <  1:5045414/70‑1 (MQ=255)
                                               cAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                                                    >  1:3910823/1‑42 (MQ=255)
                                               cAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                                                    >  1:701797/1‑42 (MQ=255)
                                               cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                         >  1:1811317/1‑69 (MQ=255)
                                               cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTa                         >  1:4094487/1‑69 (MQ=255)
                                               cAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTAc                        <  1:2124118/70‑1 (MQ=255)
                                                  ccccATCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGcc                    >  1:2273757/1‑71 (MQ=255)
                                                   ccAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGccc                   >  1:2761371/1‑71 (MQ=255)
                                                     caTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTg                 <  1:2543541/70‑1 (MQ=255)
                                                     caTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTg                 <  1:3753246/70‑1 (MQ=255)
                                                     aaTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTaa                                                <  1:4299080/40‑1 (MQ=255)
                                                      aTCGGGTCCTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGa                >  1:3363095/1‑71 (MQ=255)
                                                      aTCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt                                            >  1:2463427/1‑43 (MQ=255)
                                                       tCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAt               >  1:4835131/1‑71 (MQ=255)
                                                         ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataata                                  >  1:4172927/1‑50 (MQ=255)
                                                         ggAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt              >  1:5074099/1‑70 (MQ=255)
                                                            tccTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc          <  1:5675327/70‑1 (MQ=255)
                                                            tccTGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctc          <  1:2827269/70‑1 (MQ=255)
                                                             ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGt                          <  1:5209863/54‑1 (MQ=255)
                                                             ccTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatca         >  1:1458927/1‑71 (MQ=255)
                                                              cTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat        <  1:1215386/71‑1 (MQ=255)
                                                               tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTAc                        >  1:3606836/1‑54 (MQ=255)
                                                               tGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat        >  1:4255053/1‑70 (MQ=255)
                                                               tGAGTAATATACCGCCCCTGCAACGGATCGTAGTACCGGTGACGGTTATAGTACAGCCCTGATtcctcat        >  1:4848809/1‑70 (MQ=255)
                                                                gggtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACtcctcatca      <  1:3320751/69‑1 (MQ=255)
                                                                gAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg                                 <  1:5317765/44‑1 (MQ=255)
                                                                 aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAg                                 <  1:375271/43‑1 (MQ=255)
                                                                 aGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTcatcatcat     <  1:9140/71‑1 (MQ=255)
                                                                  gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt              >  1:1850727/1‑61 (MQ=255)
                                                                  gtgtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGAtt              >  1:3075723/1‑61 (MQ=255)
                                                                  gtgaTATACCGCCCCTGCAACGGATCGTAGTGCCGGTGACGGTTATAGTACAGCCCCGACtcctcat        <  1:4888930/67‑1 (MQ=255)
                                                                    gtTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATtcatcat        <  1:3995348/65‑1 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                  <  1:5120786/54‑1 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCt                  <  1:4608315/54‑1 (MQ=255)
                                                                     ttATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTcatcatcat     <  1:1729571/67‑1 (MQ=255)
                                                                     |                                                                     
CCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTACAGCCCTGATTCATCATCATACT  >  minE/2572667‑2572805

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