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 2,434,324 A→C 39.9% intergenic (+76/‑60) 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
*minE2,434,3240AC39.9% 49.1 / 114.9 118intergenic (+76/‑60)rhlB/gppATP‑dependent RNA helicase/guanosine pentaphosphatase/exopolyphosphatase
Reads supporting (aligned to +/- strand):  ref base A (53/18);  new base C (26/21);  total (79/39)
Fisher's exact test for biased strand distribution p-value = 4.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.61e-01

Only 100 of 127 total aligned reads displayed.

TGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAG  >  minE/2434257‑2434382
                                                                   |                                                          
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGGATGAATCCCGATGAGCTTACTgta                                                            >  1:1936751/1‑68 (MQ=255)
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:1765137/1‑68 (MQ=255)
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:1783619/1‑68 (MQ=255)
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:2487621/1‑68 (MQ=255)
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:1657245/1‑68 (MQ=255)
tGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTgta                                                            >  1:666846/1‑68 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1912806/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:3250310/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:547809/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1911652/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:759090/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1143170/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:2393373/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGt                                                      >  1:1066381/1‑67 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1852510/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:3284912/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2288047/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2095587/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2874811/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:3044032/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2534768/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2599995/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2783669/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1012446/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:434786/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:1585439/1‑69 (MQ=255)
       cTCAAAATCATTCAAACTGTATCAAAATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGa                                                    >  1:2278486/1‑69 (MQ=255)
                aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAgg                                              >  1:572273/1‑66 (MQ=255)
                aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:191365/1‑67 (MQ=255)
                aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:3150665/1‑67 (MQ=255)
                aTTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGt                                             >  1:2591323/1‑67 (MQ=255)
                      aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                      <  1:1105307/68‑1 (MQ=255)
                      aCTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGaa                                      <  1:3011308/68‑1 (MQ=255)
                            tCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGcc                               >  1:880265/1‑69 (MQ=255)
                            tCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGc                                >  1:2491450/1‑68 (MQ=255)
                                    gCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACaga                       >  1:3369359/1‑69 (MQ=255)
                                      aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:1528210/69‑1 (MQ=255)
                                      aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:2037698/69‑1 (MQ=255)
                                      aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:936750/69‑1 (MQ=255)
                                      aaGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:226303/69‑1 (MQ=255)
                                         ataatgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:2793406/67‑1 (MQ=255)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAGCGCAGAGACAg                  <  1:2243906/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:247510/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1737892/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:2970746/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1681708/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1818469/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:1889647/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:3406069/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:3231795/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:3214674/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:780215/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:238409/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:2882237/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:751995/69‑1 (MQ=38)
                                         agaATGAATCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGAATGCAGCCAACGCAGAGACAg                  <  1:645932/69‑1 (MQ=38)
                                           aatgaatCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAgaga                     <  1:327278/64‑1 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCTGGTGAAGGaa                                      >  1:316690/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1064655/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2906564/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3010971/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3013196/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:3362117/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2871977/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1615603/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1662541/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:173364/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1962081/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1250758/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2121289/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2136759/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2208510/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1177818/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1171911/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:1124526/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2658380/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGaa                                      >  1:2693560/1‑45 (MQ=255)
                                             tgaatCCCGATGCGCTTACTGTCGTAAGTGATTCAGGTGAAGGa                                       >  1:523442/1‑44 (MQ=38)
                                                 tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:2356100/68‑1 (MQ=255)
                                                 tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:1818730/68‑1 (MQ=255)
                                                 tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:2844276/68‑1 (MQ=255)
                                                 tCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAg           <  1:410314/68‑1 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1310273/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1341376/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:949083/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:1353040/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2323889/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2403281/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2651011/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACa                   >  1:2849263/1‑58 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGa         >  1:2046397/1‑68 (MQ=255)
                                                   ccGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGa         >  1:692307/1‑68 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:355976/1‑69 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:1797738/1‑69 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:581143/69‑1 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:755567/69‑1 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  >  1:1127036/1‑69 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAagag  <  1:1075338/69‑1 (MQ=255)
                                                         aGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGAAAGATTGAAGGATGAagag  <  1:3367763/69‑1 (MQ=255)
                                                                   agtaAGTGATTGAGGTGTTAGATTGCTGCCTACACAGAGACAGTTTGAAg           <  1:1178443/50‑1 (MQ=255)
                                                                   |                                                          
TGTCATACTCAAAATCATTCAAACTGTATCAAGATGGCAAGAGAATGAATCCCGATGAGCTTACTGTAGTAAGTGATTCAGGTGAAAGAATGCAGCCAACACAGAGACAGATTGAAGGATGAAGAG  >  minE/2434257‑2434382

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