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 1,015,220 A→G 20.2% L283L (CTT→CTC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,2200AG20.2% 217.2 / 48.7 109L283L (CTT→CTC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (43/44);  new base G (11/11);  total (54/55)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

Only 100 of 109 total aligned reads displayed.

TGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTC  >  minE/1015152‑1015289
                                                                    |                                                                     
tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg                                                                     >  1:2578522/1‑71 (MQ=255)
tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg                                                                     >  1:4065708/1‑71 (MQ=255)
  aCGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAt                                                                   >  1:2604271/1‑71 (MQ=255)
  aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt                                                                   <  1:5281815/71‑3 (MQ=255)
  aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt                                                                   <  1:4418975/71‑3 (MQ=255)
    gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt                                                                 <  1:1041444/71‑1 (MQ=255)
    gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt                                                                 <  1:2163767/71‑1 (MQ=255)
     tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                                <  1:3543896/71‑1 (MQ=255)
     tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                                <  1:2860717/71‑1 (MQ=255)
     tGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct                                                                <  1:2047092/71‑3 (MQ=255)
        cAGGCGAATCACGGGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTgcg                                                             >  1:1171393/1‑71 (MQ=255)
           gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                                <  1:5482134/65‑1 (MQ=255)
           gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtt                                                                  <  1:2447383/63‑1 (MQ=255)
            cGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt                                                                <  1:2560277/64‑1 (MQ=255)
             gAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCg                                                        <  1:1013409/71‑1 (MQ=255)
             gAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCg                                                        <  1:2654855/71‑1 (MQ=255)
               aTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      >  1:1184460/1‑71 (MQ=255)
                tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:4131335/70‑1 (MQ=255)
                tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                     <  1:2829265/71‑1 (MQ=255)
                tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                     <  1:2457002/71‑1 (MQ=255)
                tCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATc                                                     <  1:3377907/71‑1 (MQ=255)
                  aCGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAg                                                   >  1:187400/1‑71 (MQ=255)
                  aCGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAg                                                   >  1:3904013/1‑71 (MQ=255)
                   cgcgGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                                  <  1:3186520/71‑1 (MQ=255)
                   cgcgAATTTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttca                                                                >  1:4392976/1‑55 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                                  <  1:828371/55‑1 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                                  <  1:2828699/55‑1 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                                  <  1:1347161/55‑1 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGttt                                                                  <  1:5358661/55‑1 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTgggc                                                            >  1:813981/1‑61 (MQ=255)
                   cgcgAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTggg                                                             >  1:3676836/1‑58 (MQ=255)
                    gcgGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                                  >  1:2286505/1‑70 (MQ=255)
                      ggATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAAt                                               >  1:2359578/1‑71 (MQ=255)
                        aTGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTc                                             <  1:2320369/71‑1 (MQ=255)
                        aTGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAt                                                                   <  1:1610945/49‑1 (MQ=255)
                         tGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCt                                            <  1:2910283/71‑1 (MQ=255)
                           tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct                                                                >  1:199845/1‑47 (MQ=19)
                           tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTcctg                                          >  1:5068033/1‑68 (MQ=255)
                           tCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTcctg                                          >  1:2990150/1‑68 (MQ=255)
                           tCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:287885/59‑1 (MQ=255)
                                 gCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAg                                    <  1:5613530/71‑1 (MQ=255)
                                  cGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAgc                                   >  1:2203378/1‑70 (MQ=255)
                                     aGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAgctg                                 <  1:4441711/70‑4 (MQ=255)
                                     aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                         >  1:4026848/1‑62 (MQ=255)
                                     aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                         >  1:2533073/1‑62 (MQ=255)
                                      gTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               >  1:5691118/1‑71 (MQ=255)
                                       tATTTATCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                                  <  1:1991901/51‑1 (MQ=255)
                                       tATTTACCGCCAAACTGCGCGCCAAGACCGAGtttc                                                                 <  1:2963042/36‑2 (MQ=12)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                                  <  1:3916370/51‑1 (MQ=255)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGc                                                  <  1:5644418/51‑1 (MQ=255)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                                 <  1:2062810/68‑1 (MQ=255)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                                 <  1:170607/68‑1 (MQ=255)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                                 <  1:5335744/68‑1 (MQ=255)
                                       tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                              <  1:4015888/71‑1 (MQ=255)
                                        aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      >  1:4286222/1‑46 (MQ=255)
                                        aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                              >  1:2587251/1‑70 (MQ=255)
                                         tttACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:548298/45‑1 (MQ=255)
                                         tttACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:3136481/45‑1 (MQ=255)
                                           tACCACCAAACTGCGCCCCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                          >  1:4337732/1‑71 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:791727/43‑1 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:2772074/43‑1 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttt                                          >  1:2086504/1‑55 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAg                                    >  1:4687202/1‑61 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                          >  1:5206192/1‑71 (MQ=255)
                                           tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                          >  1:4518929/1‑71 (MQ=255)
                                            accaccAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCa                                                 >  1:1342216/1‑47 (MQ=255)
                                            accaccAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCa                                                 >  1:3226614/1‑47 (MQ=255)
                                              caccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                                      <  1:3732206/40‑1 (MQ=255)
                                              caccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCgg                       <  1:4782366/71‑1 (MQ=255)
                                                ccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGaa                     >  1:4364390/1‑71 (MQ=255)
                                                  aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg                   >  1:3177950/1‑71 (MQ=255)
                                                   aaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGc                  >  1:5115266/1‑71 (MQ=255)
                                                   aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtttt                                         <  1:3385621/48‑1 (MQ=255)
                                                   aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGtt                                  >  1:2185789/1‑55 (MQ=255)
                                                   aaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGc                  >  1:3749115/1‑71 (MQ=255)
                                                    aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTc                                       <  1:2063972/49‑1 (MQ=255)
                                                    aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               <  1:1751104/57‑1 (MQ=255)
                                                    aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGcc                 >  1:310655/1‑71 (MQ=255)
                                                     cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTc                                       >  1:4284153/1‑48 (MQ=255)
                                                        cgcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTg               <  1:1220813/69‑1 (MQ=255)
                                                          cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGaa                     >  1:1358784/1‑61 (MQ=255)
                                                            cccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               <  1:2871839/49‑1 (MQ=255)
                                                            cccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               <  1:4259719/49‑1 (MQ=255)
                                                             ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               <  1:4973735/48‑1 (MQ=255)
                                                             ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGc        >  1:5649973/1‑71 (MQ=255)
                                                              cAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCt       >  1:4954005/1‑71 (MQ=255)
                                                               aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               >  1:1319329/1‑46 (MQ=255)
                                                               aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               >  1:1888053/1‑46 (MQ=255)
                                                               aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                               >  1:1661203/1‑46 (MQ=255)
                                                               aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCt       >  1:3869904/1‑70 (MQ=255)
                                                               aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCt       >  1:5513014/1‑70 (MQ=255)
                                                                gACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCa     <  1:2054361/71‑1 (MQ=255)
                                                                  ccAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCAtt   >  1:7295/1‑71 (MQ=255)
                                                                  ccAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCAtt   <  1:3362463/71‑1 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTcc                                      >  1:2762077/1‑35 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTcc                                      >  1:3391593/1‑35 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTcc                                      >  1:389368/1‑35 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTcc                                      >  1:4994845/1‑35 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTc  >  1:1532803/1‑71 (MQ=255)
                                                                   cAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCAAGTTCCACATcg                          >  1:4392533/1‑47 (MQ=255)
                                                                    |                                                                     
TGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTC  >  minE/1015152‑1015289

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