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 2,131,486 G→A 42.4% L488L (CTG→TTG)  deaD ← ATP‑dependent RNA helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,131,4860GA42.4% 91.4 / 178.4 234L488L (CTG→TTG) deaDATP‑dependent RNA helicase
Reads supporting (aligned to +/- strand):  ref base G (82/52);  new base A (93/6);  total (176/58)
Fisher's exact test for biased strand distribution p-value = 2.17e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 234 total aligned reads displayed.

AGCAATCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCAC  >  minE/2131421‑2131551
                                                                 |                                                                 
   aaTCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCat                                                             <  1:823499/69‑1 (MQ=255)
   aaTCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCat                                                             <  1:1251901/69‑1 (MQ=255)
   aaTCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCat                                                             <  1:42121/69‑1 (MQ=255)
    aTCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCat                                                             <  1:1887842/68‑1 (MQ=255)
      cGCACCAACTATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:297586/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:370793/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:1074259/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:1579232/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:1214798/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:1280393/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:130068/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:2538727/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:669827/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTg                                                                <  1:1387703/63‑1 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCa                                                              >  1:1715529/1‑65 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCa                                                              >  1:1657510/1‑65 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCa                                                              >  1:264960/1‑65 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCa                                                              >  1:137105/1‑65 (MQ=255)
      cGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACACCTGCa                                                              >  1:836776/1‑65 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:2068233/1‑69 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:2060457/1‑69 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:1554562/1‑69 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:445380/1‑69 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:1350797/1‑69 (MQ=255)
                     aCGAACTTCAACACCATCATCGCGGCCCACTTCAACGCGGTACAGCTGCATATCGCCAACATCacgacg                                           >  1:3129516/1‑69 (MQ=255)
                           ttCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCacgacgg                                          >  1:3063120/1‑63 (MQ=255)
                           ttCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacg                                     >  1:1182958/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTTacgac                                   >  1:1727986/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCaggac                                   >  1:462714/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                   >  1:1741076/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                   >  1:40753/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                   >  1:3402952/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                   >  1:916497/1‑69 (MQ=255)
                             cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacga                                    >  1:1030802/1‑68 (MQ=255)
                                    atcatcGCTGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            <  1:503813/69‑1 (MQ=255)
                                    atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            >  1:1534938/1‑69 (MQ=255)
                                    atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            >  1:2759492/1‑69 (MQ=255)
                                    atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            >  1:1880660/1‑69 (MQ=255)
                                    atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            >  1:1093114/1‑69 (MQ=255)
                                    atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            <  1:2002510/69‑1 (MQ=255)
                                     tcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                            <  1:2853067/68‑1 (MQ=255)
                                       atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                         >  1:2124240/1‑69 (MQ=255)
                                       atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                         >  1:3323398/1‑69 (MQ=255)
                                       atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                         >  1:3371239/1‑69 (MQ=255)
                                       atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                         >  1:549280/1‑69 (MQ=255)
                                       atcGCGGCCCACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATc                         <  1:2878666/69‑1 (MQ=255)
                                       atcGCGGCCCACTTCAAAACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATc                         <  1:1885124/69‑1 (MQ=255)
                                           cgGCCCACTTCAATGCGGTAGAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGAct                            <  1:2152240/62‑2 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCa                     >  1:2183507/1‑64 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:583418/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:85258/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:2015659/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:347671/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:1805060/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:622497/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:775405/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:3138084/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:1833776/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:1849890/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:882772/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:2723583/1‑69 (MQ=255)
                                                cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                >  1:2229389/1‑69 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGtt                                         >  1:2589087/1‑42 (MQ=38)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGtt                                         >  1:3083840/1‑42 (MQ=38)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCgcga                                    >  1:2456984/1‑47 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGCCGCGGACGATCtt                       >  1:1487737/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:3205325/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:2256770/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:2196810/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:2363160/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:2447696/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:3291242/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:650234/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:677335/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:1136503/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:1919029/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:2963171/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:207982/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:1932448/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:1981186/1‑60 (MQ=255)
                                                  cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCt                        >  1:1380731/1‑59 (MQ=255)
                                                  cTTCAATACGGTAAAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                       >  1:1011348/1‑60 (MQ=255)
                                                    tCAATGCGGTACAGCTGCATATCGCCGACATCACGACGTTCACGACGCGGACGATCTTCACGGTcacca            >  1:232237/1‑69 (MQ=255)
                                                    tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                <  1:2790212/49‑1 (MQ=255)
                                                    tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                <  1:597760/49‑1 (MQ=255)
                                                    tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                <  1:2290504/49‑1 (MQ=255)
                                                    tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                <  1:438318/49‑1 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:1689741/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:2336374/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:1355634/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:2191625/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:3090843/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:2945428/4‑69 (MQ=255)
                                                       atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc         >  1:2625988/4‑69 (MQ=255)
                                                            gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCAcgcg        >  1:2517703/1‑65 (MQ=255)
                                                            gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc    >  1:392903/1‑69 (MQ=255)
                                                            gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc    >  1:1773665/1‑69 (MQ=255)
                                                            gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc    >  1:2462906/1‑69 (MQ=255)
                                                            gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc    >  1:2689184/1‑69 (MQ=255)
                                                              aCAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCAc  >  1:2842719/1‑69 (MQ=255)
                                                                 |                                                                 
AGCAATCGCACCAACGATATGACGAACTTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCAC  >  minE/2131421‑2131551

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