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 2,434,314 A→C 37.6% intergenic (+66/‑70) rhlB → / → gpp ATP‑dependent RNA helicase/guanosine pentaphosphatase/exopolyphosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,434,3140AC37.6% 64.9 / 114.2 125intergenic (+66/‑70)rhlB/gppATP‑dependent RNA helicase/guanosine pentaphosphatase/exopolyphosphatase
Reads supporting (aligned to +/- strand):  ref base A (58/20);  new base C (26/21);  total (84/41)
Fisher's exact test for biased strand distribution p-value = 3.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

Only 100 of 138 total aligned reads displayed.

TAAATAAAAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAG  >  minE/2434246‑2434382
                                                                    |                                                                    
taaataaaAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGa                                                                      >  1:1934600/1‑69 (MQ=255)
taaataaaAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGa                                                                      >  1:3266493/1‑69 (MQ=255)
taaataaaAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGa                                                                      >  1:3267692/1‑69 (MQ=255)
    taaaAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCt                                                                   <  1:980885/68‑1 (MQ=255)
      aaaaaTGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTAc                                                                <  1:3112155/69‑1 (MQ=255)
      aaaaaTGTCATACTCAAAATCATTCAAACTGTATCAAGATCGCAAGAGAATGAATCCCGATGAGCTTAc                                                                <  1:2788844/69‑1 (MQ=255)
        aaaTGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTg                                                              <  1:2885228/69‑1 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGGATGAATCCCGATGAGCTTACTgta                                                            >  1:1936751/1‑68 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTAc                                                                <  1:1099287/64‑1 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:666846/1‑68 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:2487621/1‑68 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:1783619/1‑68 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:1657245/1‑68 (MQ=255)
           tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:875851/1‑68 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCTATGAGCTTACTGTAGTAAg                                                       >  1:2398174/1‑66 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:3250310/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1066381/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:2788273/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1911652/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:248987/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1143170/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:2393373/1‑67 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2534768/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:3044032/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:3284912/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2095587/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2288047/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:3276015/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1012446/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2599995/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2874811/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1585439/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1852510/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATCAAAATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2278486/1‑69 (MQ=255)
                  cTCAAAATCATTCAAACTGTATAAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1891664/1‑67 (MQ=255)
                           aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAgg                                              >  1:572273/1‑66 (MQ=255)
                           aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:191365/1‑67 (MQ=255)
                           aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:2591323/1‑67 (MQ=255)
                           aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:3150665/1‑67 (MQ=255)
                              cAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAg                                        <  1:3220843/69‑1 (MQ=255)
                                 aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                      <  1:1105307/68‑1 (MQ=255)
                                 aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                      <  1:3011308/68‑1 (MQ=255)
                                       tCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGcc                               >  1:880265/1‑69 (MQ=255)
                                               gCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACaga                       >  1:3369359/1‑69 (MQ=255)
                                                 aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:226303/69‑1 (MQ=255)
                                                 aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:1528210/69‑1 (MQ=255)
                                                 aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:2037698/69‑1 (MQ=255)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:2882237/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:3214674/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:2970746/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1737892/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:3406069/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1818469/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:645932/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:751995/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:780215/69‑1 (MQ=38)
                                                    agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:108955/69‑1 (MQ=38)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3362117/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1171911/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1177818/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1250758/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:499498/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:577971/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3013196/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3010971/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1064655/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1962081/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2136759/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2208510/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:173364/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1659254/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1662541/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2658380/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2693560/1‑45 (MQ=255)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGa                                       >  1:2868018/1‑44 (MQ=38)
                                                        tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGa                                       >  1:523442/1‑44 (MQ=38)
                                                            tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:2844276/68‑1 (MQ=255)
                                                            tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:410314/68‑1 (MQ=255)
                                                            tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:2356100/68‑1 (MQ=255)
                                                            tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:1818730/68‑1 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2909488/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1310273/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:949083/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2113112/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2849263/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1353040/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2220045/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2323889/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1341376/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2403281/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2651011/1‑58 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGa         >  1:692307/1‑68 (MQ=255)
                                                              ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGa         >  1:2046397/1‑68 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:581143/69‑1 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:355976/1‑69 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:1797738/1‑69 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:755567/69‑1 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:1762841/69‑1 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:1127036/1‑69 (MQ=255)
                                                                    aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGAAAGATTGAAGGATGAagag  <  1:3367763/69‑1 (MQ=255)
                                                                    |                                                                    
TAAATAAAAAATGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAG  >  minE/2434246‑2434382

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