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 1,015,298 T→C 23.8% P257P (CCA→CCG)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,2980TC23.8% 152.3 / 48.1 88P257P (CCA→CCG) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (36/31);  new base C (8/13);  total (44/44)
Fisher's exact test for biased strand distribution p-value = 3.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01

TTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCAC  >  minE/1015232‑1015368
                                                                  |                                                                      
ttCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTgg                                                                      >  1:5049742/1‑69 (MQ=255)
ttCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTgg                                                                      >  1:5237853/1‑69 (MQ=255)
  cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                                                                  >  1:1156936/1‑71 (MQ=255)
  cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                                                                  >  1:841212/1‑71 (MQ=255)
  cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                                                                  >  1:825667/1‑71 (MQ=255)
  cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                                                                  >  1:5597289/1‑71 (MQ=255)
   ttccagcagTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAg                                                                   <  1:2850847/66‑1 (MQ=255)
      cagcagTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtca                                                               <  1:3529388/70‑1 (MQ=255)
       aGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGTCAGTtcat                                                              <  1:462331/70‑1 (MQ=255)
       aGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcat                                                              >  1:2260021/1‑70 (MQ=255)
       aGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcat                                                              >  1:1069328/1‑70 (MQ=255)
       aGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcat                                                              <  1:3075955/70‑1 (MQ=255)
       aGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCCTTGGCAGTtcat                                                              <  1:3081069/70‑1 (MQ=255)
        gCAGTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcatcg                                                            <  1:752292/71‑2 (MQ=255)
          aaTTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcatca                                                            >  1:2610039/1‑69 (MQ=255)
              cTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTAt                                                      >  1:750885/1‑71 (MQ=255)
                ttttCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTAtt                                                     >  1:3862745/1‑70 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTTATCGTAATagt                                                     <  1:17031/68‑3 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTaa                                                         >  1:3190261/1‑63 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagtg                                                    <  1:2284907/69‑4 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagtg                                                    <  1:5569910/69‑4 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagtg                                                    <  1:4404743/69‑4 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagt                                                     <  1:4515649/68‑3 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagt                                                     <  1:4736138/68‑3 (MQ=255)
                  ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagt                                                     <  1:4292728/68‑3 (MQ=255)
                   tCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTcgc                                                 >  1:983451/1‑71 (MQ=255)
                        ttCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAg                                            >  1:4799669/1‑71 (MQ=255)
                          ccACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAg                                                                   >  1:3122701/1‑46 (MQ=255)
                          ccACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcatca                                                            >  1:5571181/1‑53 (MQ=255)
                          ccACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGc                                           >  1:404647/1‑70 (MQ=255)
                          ccACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGc                                           >  1:3446307/1‑70 (MQ=255)
                              aTCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAg                                                         >  1:4489761/1‑52 (MQ=255)
                              aTCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGtt                                      >  1:4543378/1‑71 (MQ=255)
                              aTCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtc                                                                <  1:3609211/45‑1 (MQ=255)
                              aTCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtc                                                                <  1:5339815/45‑1 (MQ=255)
                               tCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcat                                                              <  1:4574071/46‑1 (MQ=255)
                               tCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGttt                                     <  1:694299/71‑1 (MQ=255)
                               tCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGttt                                     <  1:3077542/71‑1 (MQ=255)
                               tCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGttt                                     <  1:1834510/71‑1 (MQ=255)
                               tCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGttt                                     >  1:4235186/1‑71 (MQ=255)
                                cgcgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGtt                                                                 >  1:524866/1‑42 (MQ=255)
                                cgcgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGtt                                                                 >  1:751471/1‑42 (MQ=255)
                                cgcgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGtt                                                                 >  1:4184905/1‑42 (MQ=255)
                                cgcgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGtt                                                                 >  1:476484/1‑42 (MQ=255)
                                cgcgGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGt                                                                  >  1:4101945/1‑41 (MQ=25)
                                cgcgGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcatc                                                             >  1:2080178/1‑46 (MQ=255)
                                cgcgGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcat                                                              >  1:5415063/1‑45 (MQ=255)
                                 gcgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGaa                                             >  1:2008294/1‑61 (MQ=255)
                                 gcgGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTa                                                          >  1:5257797/1‑48 (MQ=255)
                                 gcgGAACGCCTGACCATGTTCGTTACCTTCCGTCGGc                                                                     >  1:5326464/1‑37 (MQ=16)
                                 gcgGAACGCCCGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTa                                                          >  1:3393111/1‑48 (MQ=19)
                                  cgGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCAc                                  <  1:2302416/71‑1 (MQ=255)
                                  cgGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcat                                                              <  1:5137597/43‑1 (MQ=25)
                                   ggAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAg                                                         <  1:2423036/47‑1 (MQ=255)
                                     aaCGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTa                                                       >  1:1589301/1‑47 (MQ=255)
                                     aaCGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTa                                                       >  1:2587117/1‑47 (MQ=255)
                                     aaCGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTa                                                       >  1:5109643/1‑47 (MQ=255)
                                        gCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:5389410/71‑1 (MQ=255)
                                         ccTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:4389633/70‑1 (MQ=255)
                                         ccTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            >  1:1930855/1‑70 (MQ=255)
                                         ccTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            >  1:2418531/1‑70 (MQ=255)
                                             aCCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGt                       <  1:3751543/71‑1 (MQ=255)
                                               cGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTc                     <  1:1029168/71‑1 (MQ=255)
                                                 tGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:1056117/62‑1 (MQ=255)
                                                 tGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:2469337/62‑1 (MQ=255)
                                                 tGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:4152522/62‑1 (MQ=255)
                                                  gCTCATTCCCTTCCGTTGGCAGTTCATCATAGTAt                                                      >  1:1864333/1‑35 (MQ=255)
                                                  gCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtt                              <  1:4769520/59‑1 (MQ=255)
                                                  gCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGtt                  >  1:2281909/1‑71 (MQ=255)
                                                  gCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGtt                  >  1:5600145/1‑71 (MQ=255)
                                                     cATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGcc                                          <  1:3693853/44‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGTAAGCCa                                         <  1:739269/44‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCa                                         <  1:1418580/44‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCa                                         <  1:62990/44‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTc                <  1:4961902/69‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTc                <  1:898968/69‑1 (MQ=255)
                                                      aTTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCt               >  1:147904/1‑70 (MQ=255)
                                                       ttCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCa                                         <  1:3998619/43‑1 (MQ=255)
                                                       ttCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCt               >  1:2425928/1‑69 (MQ=255)
                                                        tCCCTTCCGTCGGCAGTTCATCGTAATAGTGAGCGCTTGCTAACTTGACGGTTTTCAGGTTGGTTTccg              >  1:2212573/1‑67 (MQ=255)
                                                          ccTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAg           <  1:3626555/70‑1 (MQ=255)
                                                          ccTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAg           <  1:5404010/70‑1 (MQ=255)
                                                          ccTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAg           <  1:1177108/70‑1 (MQ=255)
                                                          ccTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAg           <  1:5056388/70‑1 (MQ=255)
                                                           cTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAg           <  1:4485363/69‑1 (MQ=255)
                                                            ttCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTc                                    <  1:2943563/43‑1 (MQ=255)
                                                               cGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTc     >  1:3795441/1‑71 (MQ=255)
                                                               cGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTc     <  1:1543930/71‑1 (MQ=255)
                                                                 ttGTCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:3827362/46‑1 (MQ=255)
                                                                 ttGGCAGTTCATCATAGTATTTCGCGGAAGCCAGtt                                      <  1:4443503/36‑1 (MQ=255)
                                                                 ttGGCAGTTCATCATAGTATTTCGCGGAAGCCAGtt                                      <  1:3484738/36‑1 (MQ=255)
                                                                 ttGGCAGTTCATCATAGTATTTCGCGGAAGCCAGtt                                      <  1:963552/36‑1 (MQ=255)
                                                                 ttGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGtttt                            <  1:4578205/46‑1 (MQ=255)
                                                                 ttGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTcca   >  1:2912347/1‑71 (MQ=255)
                                                                  tGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTccac  >  1:5304233/1‑71 (MQ=255)
                                                                  |                                                                      
TTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGCCAGTTTCACCGTTTTAAGGTTCGTTTCTGCAGAAGTTCCAC  >  minE/1015232‑1015368

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