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 2,251,690 A→C 22.6% intergenic (+38/+372) thiH → / ← htrC thiamin biosynthesis ThiGH complex subunit/heat shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,251,6900AC22.6% 137.7 / 42.1 93intergenic (+38/+372)thiH/htrCthiamin biosynthesis ThiGH complex subunit/heat shock protein
Reads supporting (aligned to +/- strand):  ref base A (44/28);  new base C (9/12);  total (53/40)
Fisher's exact test for biased strand distribution p-value = 2.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGTAGTGCCGTCAGCAGG  >  minE/2251634‑2251755
                                                        |                                                                 
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:2945229/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:3380532/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:173149/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:308216/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:1344070/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:207015/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:825059/1‑69 (MQ=255)
cgcCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaa                                                       >  1:594730/1‑69 (MQ=255)
  ccTAGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaaaa                                                     <  1:3315495/69‑1 (MQ=255)
   cTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGaaaaa                                                     <  1:2522185/68‑1 (MQ=255)
    tCGCAAAGGCCATGAGACAGATTGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:109259/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGaaaaa                                                     >  1:1633103/1‑67 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:664937/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:2000144/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:771131/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:1179340/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:115722/1‑68 (MQ=255)
    tCGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:2677497/1‑68 (MQ=255)
    gcGCAAAGGCCATGAGACAGAATGTAAGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAAc                                                    >  1:3118939/2‑68 (MQ=255)
     cGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAAc                                                    >  1:3134089/1‑67 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACTGAAGATGAAAAACGCAAgg                                              >  1:97365/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:102148/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:1871742/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:1698339/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:3069304/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:1641012/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:3349693/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:355004/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:1023693/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:579835/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:1305405/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAgg                                              >  1:887197/1‑69 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg                                               >  1:3067248/1‑68 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg                                               >  1:106152/1‑68 (MQ=255)
         aaGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg                                               >  1:303876/1‑68 (MQ=255)
           gACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg                                               >  1:1008803/1‑66 (MQ=255)
            aCTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAg                                               >  1:279425/1‑65 (MQ=255)
            aCTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGgttg                                           >  1:275504/1‑69 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               >  1:3229292/1‑47 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:952811/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               >  1:2997378/1‑47 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:3111556/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               >  1:2924156/1‑47 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:993033/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:1101626/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:260070/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:1494157/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               <  1:2649076/47‑1 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               >  1:1566909/1‑47 (MQ=255)
              tATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGa                                                               >  1:1281199/1‑47 (MQ=255)
                tGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGgttgtt                                         >  1:147443/1‑67 (MQ=255)
                            tAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtt                           >  1:1168182/1‑69 (MQ=255)
                            tAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtt                           >  1:2886021/1‑69 (MQ=255)
                            tAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtt                           >  1:1489682/1‑69 (MQ=255)
                            tAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtt                           >  1:3272474/1‑69 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttt                         >  1:309683/1‑69 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:3052906/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:361780/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:146960/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:1185562/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:2581526/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:2981012/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:1195535/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:3143088/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:1199368/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:1569576/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:1408594/68‑1 (MQ=255)
                              aGAACGTAAATTTATTCCGAGCAGCTCCGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGttt                          <  1:2249298/68‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACTGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:1310989/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:3148762/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:3111214/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:3202286/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:594184/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:1489724/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:3377261/69‑1 (MQ=255)
                                aaCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       <  1:2912077/69‑1 (MQ=255)
                                 aCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       >  1:3262807/1‑68 (MQ=255)
                                 aCGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGtttttt                       >  1:3008918/1‑68 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGc                                   >  1:3149951/1‑51 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGc                                   >  1:486349/1‑51 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGc                                   >  1:1810042/1‑51 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGc                                   >  1:2938468/1‑51 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:2109882/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:2318255/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:639937/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:2391922/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:941997/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:2875255/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:1119613/69‑1 (MQ=255)
                                      aaTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:2633494/69‑1 (MQ=255)
                                       aTTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGt                 <  1:3002203/68‑1 (MQ=255)
                                                     gCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGTAGTGCCGTCAGCAgg  <  1:582770/69‑1 (MQ=255)
                                                     gCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGTAGTGCCGTCAGCAgg  <  1:2554401/69‑1 (MQ=255)
                                                        |                                                                 
CGCCTCGCAAAGACTATGAGACGGAATGTAAGAACGTAAATTTATTCCGAGCCGCTACGGAAGATGAAAAACGCAAGGTTGTTGAAAGCGTTGTGTTTTTTTATGGTAGTGCCGTCAGCAGG  >  minE/2251634‑2251755

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