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 1,390,615 A→G 71.7% Q249Q (CAA→CAG)  nfo → endonuclease IV with intrinsic 3'‑5' exonuclease activity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,390,6150AG71.7% 178.8 / 80.5 120Q249Q (CAA→CAG) nfoendonuclease IV with intrinsic 3'‑5' exonuclease activity
Reads supporting (aligned to +/- strand):  ref base A (17/17);  new base G (42/44);  total (59/61)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 120 total aligned reads displayed.

CGCGTTGACCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCAGAAGAG  >  minE/1390547‑1390681
                                                                    |                                                                  
cgcgTTGACCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGga                                                                  >  1:2416076/1‑71 (MQ=255)
 gcgTTGACCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGga                                                                  >  1:5041463/1‑70 (MQ=255)
     tGACCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGAcc                                                             >  1:2903703/1‑71 (MQ=255)
       aCCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGt                                                           >  1:498833/1‑71 (MQ=255)
       aCCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGt                                                           >  1:576348/1‑71 (MQ=255)
        ccGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGtt                                                          <  1:3903613/71‑1 (MQ=255)
          gCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        <  1:3889519/71‑1 (MQ=255)
          gCCATCATAGCCTCGGAGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        <  1:2305848/71‑1 (MQ=255)
           ccATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTc                                                        >  1:786291/1‑70 (MQ=255)
           ccATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTc                                                        >  1:1728552/1‑70 (MQ=255)
             atcatAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGAc                                                     <  1:2718316/71‑1 (MQ=255)
              tcatAGCCTCGTTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCg                                                       <  1:5527570/68‑1 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGttt                                                         >  1:5138435/1‑64 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      >  1:1330758/1‑67 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACgg                                                   <  1:3066369/70‑1 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACgg                                                   <  1:1225596/70‑1 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACgg                                                   <  1:3197701/70‑1 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACgg                                                   <  1:4004741/70‑1 (MQ=255)
                atAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACgg                                                   >  1:750959/1‑70 (MQ=255)
                 tAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCa                                                 >  1:1300139/1‑71 (MQ=255)
                   gCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCAt                                                >  1:1660334/1‑70 (MQ=255)
                     cTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTcc                                             <  1:27343/71‑1 (MQ=255)
                      tCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCg                                            >  1:5316967/1‑71 (MQ=255)
                      tCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCg                                            >  1:3450932/1‑71 (MQ=255)
                      tCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCg                                            >  1:5581133/1‑71 (MQ=255)
                        ggTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCg                                            <  1:3146161/69‑1 (MQ=255)
                        ggTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCg                                            <  1:2962635/69‑1 (MQ=255)
                        ggTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGc                                           <  1:813370/70‑1 (MQ=255)
                         gTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTg                                         <  1:4979206/71‑1 (MQ=255)
                         gTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTg                                         <  1:735100/71‑1 (MQ=255)
                           gAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGAt                                       >  1:4717645/1‑71 (MQ=255)
                            aaGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATc                                      >  1:723889/1‑71 (MQ=255)
                              ggCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGa                                                      >  1:1017968/1‑53 (MQ=255)
                              ggCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGAc                                                     <  1:1585931/54‑1 (MQ=255)
                               gCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTc                                   <  1:1228278/71‑1 (MQ=255)
                                cAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCg                                  <  1:3199164/71‑1 (MQ=255)
                                cAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCg                                  <  1:4049172/71‑1 (MQ=255)
                                cAATATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCg                                  <  1:1500872/71‑1 (MQ=255)
                                 aaTATCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCg                                  <  1:1681627/70‑1 (MQ=255)
                                  atatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                <  1:2901670/71‑1 (MQ=255)
                                  atatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                <  1:5509785/71‑1 (MQ=255)
                                  atatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                <  1:3782188/71‑1 (MQ=255)
                                  atacCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                <  1:5103647/71‑1 (MQ=255)
                                   tatCGGTCATGATGCTTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTcc                                             <  1:2392664/57‑1 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGga                                                                  <  1:700072/36‑1 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      <  1:760549/48‑1 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      <  1:4196756/48‑1 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      >  1:856033/1‑48 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      >  1:1494487/1‑48 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      <  1:1839163/48‑1 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaga                               >  1:4373681/1‑69 (MQ=255)
                                   tatCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaaa                               >  1:4558910/1‑71 (MQ=255)
                                    atCGGTCATGATGCGTTCCGCTGGATCATGCAGga                                                                  >  1:2449868/1‑35 (MQ=255)
                                    atCGGTCATGATGCGTTCCGCTGGATCATGCAGga                                                                  >  1:4757218/1‑35 (MQ=255)
                                    atCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                <  1:1891539/69‑1 (MQ=255)
                                    atCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTc                                                        <  1:3050954/45‑1 (MQ=255)
                                     tCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGa                                                      >  1:2784693/1‑46 (MQ=255)
                                     tCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAAc                              <  1:5107569/70‑1 (MQ=255)
                                     tCGGTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAAc                              >  1:4496410/1‑70 (MQ=255)
                                     tCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                >  1:5283917/1‑68 (MQ=255)
                                     tCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaa                                >  1:2938968/1‑68 (MQ=255)
                                        gTCATGATGCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATc                          <  1:5574596/71‑1 (MQ=255)
                                            tgatgCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGAt                                       >  1:5663160/1‑54 (MQ=255)
                                             gatgCGTTCCGCTGGATCATGCAAGACGACCGTTTc                                                        <  1:5307203/36‑1 (MQ=255)
                                             gatgCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTc                                              >  1:1104639/1‑46 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        >  1:4437023/1‑35 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        >  1:328129/1‑35 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        >  1:42690/1‑35 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        >  1:4956359/1‑35 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTc                                                        >  1:3374223/1‑35 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCg                    <  1:4317806/71‑1 (MQ=255)
                                              atgCGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCg                    <  1:2004999/71‑1 (MQ=255)
                                                 cGTTCCGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCgg                   >  1:1657547/1‑69 (MQ=255)
                                                   ttCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTcc                                             <  1:4896837/41‑1 (MQ=255)
                                                   ttCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTcc                                             <  1:3162277/41‑1 (MQ=255)
                                                   ttCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCaa                        <  1:505533/62‑1 (MQ=255)
                                                     ccGCTGGATCATGCAGGACGACCGTTTCGACGGCAtt                                               >  1:1678386/1‑37 (MQ=255)
                                                     ccGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCt                                          >  1:4733310/1‑42 (MQ=255)
                                                     ccGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCt                                          >  1:1793592/1‑42 (MQ=255)
                                                     ccGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCt                                          >  1:5409857/1‑42 (MQ=255)
                                                      cGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCt             <  1:5354652/70‑1 (MQ=255)
                                                      cGCTGGATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTg            >  1:5291433/1‑71 (MQ=255)
                                                      cGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTg            >  1:118005/1‑71 (MQ=255)
                                                         tGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTggg          >  1:5118190/1‑70 (MQ=255)
                                                           gATCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCag       <  1:4833217/71‑1 (MQ=255)
                                                             tCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCa                         <  1:5354149/51‑1 (MQ=255)
                                                             tCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCa                         <  1:2341464/51‑1 (MQ=255)
                                                             tCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCa                         <  1:3851013/51‑1 (MQ=255)
                                                             tCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCa                         <  1:4424241/51‑1 (MQ=255)
                                                             tCATGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCa                         <  1:3613379/51‑1 (MQ=255)
                                                               aTGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGaaa                               >  1:3122490/1‑43 (MQ=255)
                                                               aTGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCAt                           >  1:5190526/1‑47 (MQ=255)
                                                               aTGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATc                          >  1:304554/1‑48 (MQ=255)
                                                               aTGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGa                  >  1:4190338/1‑56 (MQ=255)
                                                               aTGCAGGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCagaa     >  1:4558559/1‑69 (MQ=255)
                                                               aTGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCagaag    <  1:5399835/70‑1 (MQ=255)
                                                               aTGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCagaag    <  1:2257283/70‑1 (MQ=255)
                                                                  cAAGACGACCGTTTCGACGGCATTCCGCTGATCCTc                                   >  1:721951/1‑36 (MQ=255)
                                                                  cAAGACGACCGTTTCGACGGCATTCCGCTGATCCTc                                   >  1:3319053/1‑36 (MQ=255)
                                                                  cAAGACGACCGTTTCGACGGCATTCCGCTGATCCTc                                   >  1:3335036/1‑36 (MQ=255)
                                                                    |                                                                  
CGCGTTGACCGCCATCATAGCCTCGGTGAAGGCAATATCGGTCATGATGCGTTCCGCTGGATCATGCAAGACGACCGTTTCGACGGCATTCCGCTGATCCTCGAAACCATCAACCCGGATATCTGGGCAGAAGAG  >  minE/1390547‑1390681

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