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 1,924,613 T→C 24.9% R326R (CGT→CGC)  galR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,924,6130TC24.9% 99.7 / 28.9 84R326R (CGT→CGC) galRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (39/24);  new base C (7/14);  total (46/38)
Fisher's exact test for biased strand distribution p-value = 4.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGGCGCTGGCGGATAATCGCCCTCTCCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAA  >  minE/1924545‑1924677
                                                                    |                                                                
ttGGCGCTGGCGGATAATCGCCCTCTCCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTAcgtcgt                                                                  <  1:1132843/69‑1 (MQ=255)
     gcTGGCGGATAATCGCCCTCTCCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTc                                                             >  1:2146506/1‑69 (MQ=255)
      cTGGCGGATAATCGCCCTCTCCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCa                                                            <  1:1609288/69‑1 (MQ=255)
                         tcCCGGAAATCACTGATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTgg                                         >  1:3199239/1‑69 (MQ=255)
                         tcCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTgg                                         >  1:397319/1‑69 (MQ=255)
                         tcCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTgg                                         >  1:3313374/1‑69 (MQ=255)
                         tcCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTAAGTGTCAACTCCGTCGCTgg                                         >  1:1684450/1‑69 (MQ=255)
                                aaTCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCaa                                   >  1:926894/1‑68 (MQ=255)
                                aaTCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCaa                                   >  1:2964007/1‑68 (MQ=255)
                                aaTCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCaa                                   >  1:390990/1‑68 (MQ=255)
                                aaTCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCaa                                   >  1:1783575/1‑68 (MQ=255)
                                aaTCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCaa                                   >  1:1729639/1‑68 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:3169448/69‑1 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:2696360/69‑1 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:2235901/69‑1 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:186177/69‑1 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:3432738/69‑1 (MQ=255)
                                    aCTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              <  1:1410066/69‑1 (MQ=255)
                                        aTGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTcatcat                           >  1:1938260/1‑68 (MQ=255)
                                          gTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        <  1:3191795/69‑1 (MQ=255)
                                          gTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        <  1:2024871/69‑1 (MQ=255)
                                          gTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        <  1:3165141/69‑1 (MQ=255)
                                          gTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        <  1:1917682/69‑1 (MQ=255)
                                          gTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        <  1:3070475/69‑1 (MQ=255)
                                           tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATgta                        >  1:2010254/1‑66 (MQ=255)
                                           tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        >  1:2592182/1‑68 (MQ=255)
                                           tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        >  1:2802990/1‑68 (MQ=255)
                                           tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        >  1:663196/1‑68 (MQ=255)
                                           tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCa                        >  1:3052139/1‑68 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:1890006/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:3088414/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:1335767/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:2121388/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:548814/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:2184103/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:2209970/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:2211213/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:1547485/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:1573471/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:727861/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:1646667/1‑60 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGc                         >  1:1017490/1‑65 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:1569993/1‑69 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:3436039/1‑69 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:3239863/1‑69 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:1614964/1‑69 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:36776/1‑69 (MQ=255)
                                             tttAGTCCGACGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAcc                     >  1:3040003/1‑69 (MQ=255)
                                             tttAGTCCGACACTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcat                              >  1:613011/1‑60 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATGATGCAACCAGCg                 <  1:916140/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:1010338/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:1587857/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:402765/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:1874783/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:1289510/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:2020780/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:2853434/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:2822149/68‑1 (MQ=255)
                                                  tCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCg                 <  1:918548/68‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1304438/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:422925/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:677992/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1406894/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1450337/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1274596/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:950308/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:3313036/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:3307600/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1826458/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:1832559/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:3163973/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:2845441/69‑1 (MQ=255)
                                                       cGCTGGTACGTCGCCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           <  1:2013332/69‑1 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGTAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:3096308/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCGACCAGCGACTAAc           >  1:3002967/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:903960/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:791201/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:747/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:907957/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:703436/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:3380959/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:1919546/1‑68 (MQ=255)
                                                        gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAc           >  1:2293466/1‑68 (MQ=255)
                                                              aCGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt     <  1:3038549/68‑1 (MQ=255)
                                                              aCGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt     <  1:464357/68‑1 (MQ=255)
                                                                 tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCGGTTaa  <  1:231699/68‑1 (MQ=255)
                                                                 tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTaa  <  1:2851633/68‑1 (MQ=255)
                                                                 tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTaa  <  1:1640262/68‑1 (MQ=255)
                                                                 tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTaa  <  1:229925/68‑1 (MQ=255)
                                                                    |                                                                
TTGGCGCTGGCGGATAATCGCCCTCTCCCGGAAATCACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAA  >  minE/1924545‑1924677

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