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 2,569,847 C→T 13.6% P39P (CCC→CCT)  yibI → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,569,8470CT13.6% 210.7 / 20.5 81P39P (CCC→CCT) yibIpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (46/24);  new base T (8/3);  total (54/27)
Fisher's exact test for biased strand distribution p-value = 7.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

GTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTC  >  minE/2569779‑2569914
                                                                    |                                                                   
gTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATccc                                                                     <  1:1767787/69‑1 (MQ=255)
gTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCa                                                                   <  1:2789212/71‑1 (MQ=255)
gTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCa                                                                   >  1:2533292/1‑71 (MQ=255)
    ttttttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                               >  1:2100605/1‑71 (MQ=255)
     tttttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                               >  1:3350040/1‑70 (MQ=255)
     tttttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                               >  1:2744494/1‑70 (MQ=255)
      ttttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCg                                                              <  1:249353/70‑1 (MQ=255)
       tttATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGAc                                                            >  1:571351/1‑71 (MQ=255)
               atcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTc                                                     <  1:1982544/70‑1 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    >  1:1920899/1‑70 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    >  1:75986/1‑70 (MQ=255)
                tcatcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    >  1:57758/1‑70 (MQ=255)
                     gcgATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                              >  1:3639745/1‑71 (MQ=255)
                      cgATACATGACATCCCTTATCTGATTGCCAAAAAGCGCACCCATCCCCATGCCGACGCTATTCATAcggag                                             >  1:916638/1‑69 (MQ=255)
                      cgATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggcg                                             <  1:1953051/71‑1 (MQ=255)
                        aTACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTAtt                                                      <  1:3783623/60‑1 (MQ=255)
                           cATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                  >  1:990938/1‑61 (MQ=255)
                           cATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                  >  1:1921031/1‑61 (MQ=255)
                           cATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCt                                         <  1:124014/70‑1 (MQ=255)
                             tGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACg                                                           >  1:1094361/1‑50 (MQ=255)
                              gACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGt                                     >  1:1269066/1‑71 (MQ=255)
                              gACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGt                                     >  1:2138577/1‑71 (MQ=255)
                                cttCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTa                                                        >  1:2725533/3‑50 (MQ=255)
                                cATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGcc                                                               <  1:276661/43‑1 (MQ=255)
                                cATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGt                                     >  1:3620947/1‑69 (MQ=255)
                                cATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGa                                   <  1:3176992/71‑1 (MQ=255)
                                cATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGa                                   <  1:1503116/71‑1 (MQ=255)
                                 aTCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    <  1:663654/53‑1 (MQ=255)
                                 aTCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAg                                  >  1:2305542/1‑71 (MQ=255)
                                  tCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                 <  1:149024/71‑1 (MQ=255)
                                   cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCAt                                                                  >  1:1496976/1‑37 (MQ=255)
                                   cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                >  1:3491670/1‑71 (MQ=255)
                                   cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                >  1:842159/1‑71 (MQ=255)
                                   cccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGcc                                >  1:843393/1‑71 (MQ=255)
                                    ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCt                               <  1:1558395/71‑1 (MQ=255)
                                      ttATCTGATTGCCAAAAAGCGCAACCATCCCCATg                                                                 >  1:990655/1‑35 (MQ=255)
                                       taccTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                            >  1:111463/4‑71 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCg                                                              >  1:2267334/1‑37 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCg                                                              >  1:3171485/1‑37 (MQ=255)
                                       tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCAt                                                   >  1:2435288/1‑48 (MQ=255)
                                        aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTAtt                                                      >  1:2335399/1‑44 (MQ=255)
                                        aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                  >  1:2613278/1‑48 (MQ=255)
                                          cTGATTGCCAAAAAGCGCAACCATCCCCATGCCGa                                                             >  1:982818/1‑35 (MQ=255)
                                           tGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcg                        >  1:3510562/1‑70 (MQ=255)
                                            gATTGCCAAAAAGCGCAACCATCCCCATGCCGACGc                                                          >  1:2152081/1‑36 (MQ=255)
                                             aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTa                          <  1:971577/67‑1 (MQ=255)
                                             aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActgt                      >  1:2019885/1‑69 (MQ=255)
                                             aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                      >  1:3013801/1‑71 (MQ=255)
                                              tttccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                     >  1:3710796/4‑71 (MQ=255)
                                              ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    <  1:2789281/40‑1 (MQ=255)
                                              ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcgg                                               >  1:24152/1‑45 (MQ=255)
                                              ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcgg                                               >  1:428812/1‑45 (MQ=255)
                                               tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCa                                                    >  1:3616810/1‑39 (MQ=255)
                                               tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                     <  1:524203/70‑1 (MQ=255)
                                               tGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCa                                                    >  1:3333080/1‑39 (MQ=16)
                                                 ccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGc                    <  1:3466348/69‑1 (MQ=255)
                                                 ccAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCAt                  >  1:3241722/1‑71 (MQ=255)
                                                   aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                            >  1:3375704/1‑59 (MQ=255)
                                                   aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                            >  1:2014367/1‑59 (MQ=255)
                                                   aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                >  1:564705/1‑71 (MQ=255)
                                                    aaaaGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                              <  1:1183526/40‑1 (MQ=255)
                                                    aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                >  1:937618/1‑70 (MQ=255)
                                                     aaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                            >  1:2508762/1‑57 (MQ=255)
                                                     aaaGCGCAACCATCCCCATGCCGACGCTATTCATAcgg                                               >  1:2275429/1‑38 (MQ=255)
                                                     aaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTa              >  1:3159904/1‑71 (MQ=255)
                                                      aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTa              >  1:2022477/1‑70 (MQ=255)
                                                      aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTAt             <  1:890090/71‑1 (MQ=255)
                                                       aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc            <  1:985524/71‑1 (MQ=255)
                                                       aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc            <  1:1049032/71‑1 (MQ=255)
                                                       aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc            >  1:3358137/1‑71 (MQ=255)
                                                        gcgcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                 >  1:2446425/1‑49 (MQ=255)
                                                          gcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTg          <  1:2839573/70‑1 (MQ=255)
                                                           cAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGc        <  1:1188419/71‑1 (MQ=255)
                                                             atcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGcc       <  1:425152/68‑1 (MQ=255)
                                                             aCCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCg      >  1:188367/1‑71 (MQ=255)
                                                              ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt     >  1:415982/1‑71 (MQ=255)
                                                               cATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGtt    >  1:948653/1‑71 (MQ=255)
                                                                aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttt   >  1:2523582/1‑71 (MQ=255)
                                                                aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGtt    <  1:1663610/70‑1 (MQ=255)
                                                                aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATATGGCCGtt    <  1:2218898/70‑1 (MQ=255)
                                                                 tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc  <  1:1351690/71‑1 (MQ=255)
                                                                 tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc  <  1:2416691/71‑1 (MQ=255)
                                                                    ccATGCCGACGCTATTAATACGGCGGGCTGGGTGAGCCTGCTTACTCTGCATGtt               <  1:2461933/55‑1 (MQ=255)
                                                                    |                                                                   
GTGATTTTTTATGGAATCATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTC  >  minE/2569779‑2569914

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