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 2,605,140 A→T 57.1% V94V (GTT→GTA)  uspA ← universal stress global response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,605,1400AT57.1% 31.8 / 87.9 84V94V (GTT→GTA) uspAuniversal stress global response regulator
Reads supporting (aligned to +/- strand):  ref base A (12/24);  new base T (37/11);  total (49/35)
Fisher's exact test for biased strand distribution p-value = 1.10e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTAGTGGAA  >  minE/2605073‑2605203
                                                                   |                                                               
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:1017626/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:922869/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:540363/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:2926073/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:2672617/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:2560357/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:251276/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:229245/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:1226408/68‑1 (MQ=255)
tCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGa                                                                 <  1:1291743/68‑1 (MQ=255)
    gAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCt                                                             <  1:2614562/68‑1 (MQ=255)
    gAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCt                                                             <  1:2469304/68‑1 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCttg                                                           >  1:1566456/1‑66 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2145092/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:1237561/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2575622/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2234051/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2184114/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2165820/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:2114765/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:355740/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTgg                                                           >  1:1416592/1‑68 (MQ=255)
      aGTCCTGGTGGTGACCACAAACCACCAGATCCATATCGTATTTCTTGATTGCATCGACCAGTACCTg                                                            >  1:294916/1‑67 (MQ=255)
                gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                                                >  1:1946765/1‑69 (MQ=255)
                gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                                                >  1:287552/1‑69 (MQ=255)
                gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                                                >  1:2098185/1‑69 (MQ=255)
                gtgACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTcgcc                                                >  1:3344517/1‑69 (MQ=255)
                                 aaTCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGttt                               <  1:2569351/69‑1 (MQ=255)
                                 aaTCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGttt                               <  1:1663532/69‑1 (MQ=255)
                                 aaTCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGttt                               <  1:1684109/69‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:614975/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:2806898/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:1674551/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:1623141/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:1785107/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:2497888/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:2167853/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:636454/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:618938/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:571291/65‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:318382/68‑1 (MQ=255)
                                       tatCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:605835/68‑1 (MQ=255)
                                        atCGTATTTCTTGATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCa                             <  1:718629/64‑1 (MQ=255)
                                        atCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:2623329/67‑1 (MQ=255)
                                         tCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGAt                        >  1:668818/1‑68 (MQ=255)
                                         tCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGG‑TTCAGTGATTg                      >  1:1001644/1‑69 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:2844913/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:3029284/1‑64 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:3132183/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:731157/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:1407645/1‑64 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:433386/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:2501766/1‑64 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:2469931/1‑64 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:245473/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:2285257/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:1679538/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:2428327/64‑1 (MQ=255)
                                           gTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:1713747/1‑64 (MQ=255)
                                           gTATTTATGGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          >  1:3435846/1‑64 (MQ=255)
                                            tATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTg                          <  1:478310/63‑1 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:3132344/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:2025149/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:1962424/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:3386643/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:3382677/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:2560152/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:2657515/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:1223497/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:2459769/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGc            >  1:2750070/1‑69 (MQ=255)
                                                    gATTGCATCGACCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGACTga            >  1:3404884/1‑68 (MQ=255)
                                                      ttGAATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTg             <  1:2071997/66‑1 (MQ=255)
                                                       tGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:2521885/69‑1 (MQ=255)
                                                       tGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:2453575/69‑1 (MQ=255)
                                                       tGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:533600/69‑1 (MQ=255)
                                                       tGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:439178/69‑1 (MQ=255)
                                                       tGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:3203610/69‑1 (MQ=255)
                                                        tcATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCAtt         <  1:1759393/67‑1 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGtt                                >  1:1474804/1‑39 (MQ=37)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGtt                                >  1:2155072/1‑39 (MQ=37)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTggg                    >  1:1944741/1‑51 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:719239/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:214753/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:1022708/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:2083268/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:3299231/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:3263478/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:2414758/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:1221045/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:284959/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGaa  >  1:2461236/1‑69 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGa   >  1:1681813/1‑68 (MQ=255)
                                                              aCCAGTACCTGGCCCAGATCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTGGTTGa   >  1:1396536/1‑68 (MQ=255)
                                                                   |                                                               
TCCAGAAGTCCTGGTGGTGACCACAAACCACCAAATCCATATCGTATTTCTTGATTGCATCGACCAGAACCTGGCCCAGGTCGCCGCTGCCGCTCAGGGTTTCAGTGATTGGGTAGCCTGCATTAGTGGAA  >  minE/2605073‑2605203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A