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 1,486,136 C→T 38.6% A392A (GCG→GCA)  nuoN ← NADH:ubiquinone oxidoreductase, membrane subunit N

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,486,1360CT38.6% 35.2 / 41.5 68A392A (GCG→GCA) nuoNNADH:ubiquinone oxidoreductase, membrane subunit N
Reads supporting (aligned to +/- strand):  ref base C (32/9);  new base T (16/10);  total (49/19)
Fisher's exact test for biased strand distribution p-value = 1.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01

GTTGTGGCCATACACCCAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGATACA  >  minE/1486075‑1486197
                                                             |                                                             
gTTGTGGCCATACACCCAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGt                                                        <  1:1978608/69‑1 (MQ=255)
              cccAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGAt                                          <  1:1303478/69‑1 (MQ=255)
              cccAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGAt                                          <  1:1744771/69‑1 (MQ=255)
              cccAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGAt                                          <  1:1505872/69‑1 (MQ=255)
               ccAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGAt                                          <  1:3020864/68‑1 (MQ=255)
                cAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATgg                                        >  1:2625313/1‑69 (MQ=255)
                cAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATgg                                        >  1:289398/1‑69 (MQ=255)
                    aCCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGc                                     >  1:529442/1‑68 (MQ=255)
                    aCCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCa                                    >  1:2826167/1‑69 (MQ=255)
                    aCCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCa                                    >  1:2893570/1‑69 (MQ=255)
                    aCCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCa                                    >  1:2996805/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:3104098/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:2095163/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:2099119/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:627019/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:2254242/1‑69 (MQ=255)
                                   gCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:1102347/1‑69 (MQ=255)
                                   gCACAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGgttgt                     >  1:2186496/1‑69 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1776244/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:2797405/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:2265813/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:261084/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:2068499/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:2398410/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1960019/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:283781/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1927520/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:3153318/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:140402/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1377962/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:680999/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1356368/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:698602/1‑68 (MQ=255)
                                         aTCAGCACCACGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCgga               >  1:1031018/1‑68 (MQ=255)
                                         aTCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            >  1:2790645/1‑56 (MQ=255)
                                         aTCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCggg               >  1:2307678/1‑69 (MQ=255)
                                         aTCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCggg               >  1:2122330/1‑69 (MQ=255)
                                            aGCACAACGATACCGCCCGCGCTGTACTGCCAGttt                                             >  1:122174/1‑36 (MQ=255)
                                            aGCACAACGATACCGCCCGCGCTGTACTGCCAGttt                                             >  1:136411/1‑36 (MQ=255)
                                            aGCACAACGATACCGCCCGCGCTGTACTGCCAGttt                                             >  1:890644/1‑36 (MQ=255)
                                            aGCACAACGATACCGCCCGCGCTGTACTGCCAGttt                                             >  1:1760843/1‑36 (MQ=255)
                                            aGCACAACGATACCGCCCGCGCTGTACTGCCAGttt                                             >  1:1934659/1‑36 (MQ=255)
                                            aGCACAACGATACCGCCAGCGCTGTACTGCCAGttt                                             >  1:2514343/1‑36 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:2405136/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:869200/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:824463/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:807394/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:1445921/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:2905308/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:2085133/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:2298439/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:2552031/47‑1 (MQ=255)
                                                  aCGATACCGCCTGCGCTGTACTGCCAGTTTGATGGTGCATCGCGAcc                            <  1:1027691/47‑1 (MQ=255)
                                                  aCGATACCGCCCGTGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      <  1:1526188/69‑1 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGaa        >  1:1475391/1‑67 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAg       >  1:176034/1‑68 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:2289706/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:2491366/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      <  1:2519757/69‑1 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:2533211/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:425396/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:1497097/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      >  1:2729831/1‑69 (MQ=255)
                                                  aCGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      <  1:1897353/69‑1 (MQ=255)
                                                  aCGATACAGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGa      <  1:2613675/69‑1 (MQ=255)
                                                     aTACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGATAc   >  1:92412/1‑69 (MQ=255)
                                                     aTACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGATAc   >  1:241965/1‑69 (MQ=255)
                                                     aTACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCC‑GGGCGTGAAGATACa  >  1:1501287/1‑69 (MQ=255)
                                                             |                                                             
GTTGTGGCCATACACCCAGCACCAGTACCAACAGTGCAGAGATCAGCACAACGATACCGCCCGCGCTGTACTGCCAGTTTGATGGTGCATCGCGACCCGGTTGTTCCGGGGCGTGAAGATACA  >  minE/1486075‑1486197

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