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 1,513,603 A→C 43.9% L92L (CTT→CTG)  ubiX ← 3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,513,6030AC43.9% 12.0 / 88.8 82L92L (CTT→CTG) ubiX3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase
Reads supporting (aligned to +/- strand):  ref base A (22/24);  new base C (25/11);  total (47/35)
Fisher's exact test for biased strand distribution p-value = 7.17e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.75e-01

ACATCTGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGATGCT  >  minE/1513550‑1513668
                                                     |                                                                 
acaTCTGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGAAAgg                                                                >  1:1061054/1‑57 (MQ=255)
acaTCTGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGAAAGGGTTttgattg                                                      >  1:1179485/1‑67 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:2073008/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:1516332/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:378061/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:2592449/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:700312/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:767710/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:2011901/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAgg                                                >  1:1086754/1‑68 (MQ=255)
     tGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAg                                                 >  1:324555/1‑67 (MQ=255)
                        ccATCAGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGc                            <  1:1421418/69‑1 (MQ=255)
                        ccATCAGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGc                            <  1:2991838/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:1627560/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:2059725/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:203301/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:3133391/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:2712400/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:359905/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:373813/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:391275/69‑1 (MQ=255)
                          aTCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:2272120/69‑1 (MQ=255)
                           tCAGTATAGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:2131682/68‑1 (MQ=255)
                           tCAGTATAGCTATGGACAATGCCGGACAGGGTTATGATTGAACAGGGTAAAATCACCATCCCCAACGt                          <  1:2920938/68‑1 (MQ=255)
                             aGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCt                        >  1:2026013/1‑68 (MQ=255)
                             aGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCt                        >  1:3279795/1‑68 (MQ=255)
                             aGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCt                        >  1:172669/1‑68 (MQ=255)
                             aGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCt                        >  1:2280/1‑68 (MQ=255)
                                 taGCTGTGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1649911/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGTACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1090709/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTttgattga                                                     >  1:944478/1‑35 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1926234/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1985818/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:2051487/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:3254714/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:2634726/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1446463/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:231500/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:221358/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:2249111/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGaa                    >  1:1059742/1‑68 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGa                     >  1:1614697/1‑67 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGa                     >  1:1502128/1‑67 (MQ=255)
                                 taGCTATGGACAATGCCGGACAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAACGTCTGGa                     >  1:1288362/1‑67 (MQ=255)
                                   gatATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGa                 >  1:2304641/3‑69 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTgg                      >  1:2350745/1‑64 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:2191377/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:2633444/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:3076012/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:1012754/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:1726828/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  <  1:1950340/68‑1 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGa                 >  1:2378911/1‑69 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGa                 >  1:3425001/1‑69 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGa                 >  1:1441631/1‑69 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGa                 >  1:1658271/1‑69 (MQ=255)
                                   gCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACAATCCCCAGCGTCTGGAAAg                  <  1:1040317/68‑1 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  >  1:2088917/1‑62 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAg                  >  1:2092918/1‑62 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:1355533/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:1105780/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:3045857/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:1785766/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:2164679/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:542232/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:2595631/1‑66 (MQ=255)
                                         gACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAAcc              >  1:333244/1‑66 (MQ=255)
                                            aaTGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAaga        <  1:1349378/69‑1 (MQ=255)
                                            aaTGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAaga        <  1:404864/69‑1 (MQ=255)
                                            aaTGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAaga        <  1:2577630/69‑1 (MQ=255)
                                            aaTGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAaga        <  1:3299660/69‑1 (MQ=255)
                                            aaTGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAaga        <  1:2775353/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCTTCTGGAAAGAACCGGAAGAGAt     <  1:1129244/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:2488692/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:1337440/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:1506435/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:3137907/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:3038980/69‑1 (MQ=255)
                                               gCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGAt     <  1:1993897/69‑1 (MQ=255)
                                                  ggAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGATGCt  <  1:1430321/69‑1 (MQ=255)
                                                  ggAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGATGCt  <  1:423617/69‑1 (MQ=255)
                                                  ggAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGATGCt  <  1:682057/69‑1 (MQ=255)
                                                     |                                                                 
ACATCTGCCGCACGGGTCAGTAAGCCATCAGTATAGCTATGGACAATGCCGGAAAGGGTTTTGATTGAACAGGGTAAAATCACCATCCCCAGCGTCTGGAAAGAACCGGAAGAGATGCT  >  minE/1513550‑1513668

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