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 936,253 C→T 36.1% H230H (CAC→CAT)  fdnH → formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE936,2530CT36.1% 64.1 / 54.5 94H230H (CAC→CAT) fdnHformate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible
Reads supporting (aligned to +/- strand):  ref base C (32/28);  new base T (20/14);  total (52/42)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.89e-01

AACATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCTG  >  minE/936189‑936319
                                                                |                                                                  
aaCATGCTTGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:954946/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:3073082/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:295429/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:2742510/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:1541580/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:3191594/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:3219919/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:356164/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:1312134/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:462755/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:1685513/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:1714288/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:741854/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCg                                                                <  1:2013011/69‑1 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGcc                                                                 >  1:454684/1‑68 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCg                                                                >  1:1818763/1‑69 (MQ=255)
aaCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCg                                                                >  1:195593/1‑69 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:3097066/69‑1 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:3161162/69‑1 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:59861/69‑1 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:2382285/69‑1 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:1787883/69‑1 (MQ=255)
 aCATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGa                                                               <  1:2024369/69‑1 (MQ=255)
             cTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCt                                                   <  1:666430/69‑1 (MQ=255)
             cTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCt                                                   <  1:2165734/69‑1 (MQ=255)
             cTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCt                                                   <  1:920970/69‑1 (MQ=255)
                     cGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACg                                           <  1:2714381/69‑1 (MQ=255)
                     cGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACg                                           <  1:863789/69‑1 (MQ=255)
                     cGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACg                                           <  1:2453659/69‑1 (MQ=255)
                      ggAAGGGGTCGGTGGTAGGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2044433/1‑69 (MQ=25)
                      ggAAGGGGTCGGTGGTACGCACGTTTTGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2440953/1‑69 (MQ=25)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCatg                                           >  1:2888418/1‑66 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCatg                                           >  1:2163833/1‑66 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2997930/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:3433576/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2544856/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:3365907/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:1431720/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2703546/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:3108821/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:1290485/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:1663661/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:217634/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:682985/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:700071/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:762509/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:193457/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCATGCCGATCAGCCGGAGCTGTATCATgg                                          >  1:2897203/1‑69 (MQ=255)
                      ggAAGGGGTCGGTGGTAAGCACGTTATGTACGTGCTGCATCATGCCGATCAGCAGGAGCTGTATCatg                                           >  1:625041/1‑66 (MQ=25)
                             gTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:1754126/1‑68 (MQ=255)
                             gTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:1025330/1‑68 (MQ=255)
                             gTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:2183263/1‑68 (MQ=255)
                             gTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:860682/1‑68 (MQ=255)
                                    gtACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGAt                             >  1:3242493/1‑68 (MQ=255)
                                    gtACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGAt                             >  1:387317/1‑68 (MQ=255)
                                    gtACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGAt                             >  1:817731/1‑68 (MQ=255)
                                    gtACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGAt                             >  1:824951/1‑68 (MQ=255)
                                      aCGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:1608516/1‑59 (MQ=255)
                                      aCGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:1612326/1‑59 (MQ=255)
                                      aCGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:106259/1‑59 (MQ=255)
                                      aCGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:1899644/1‑59 (MQ=255)
                                      aCGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGcc                                    >  1:2290653/1‑59 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:272707/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:1563961/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:929435/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:1977486/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:268316/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:2564954/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:1802839/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:2076696/69‑1 (MQ=255)
                                            gTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATc                    <  1:1759809/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:113190/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:927376/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:1091321/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:1095298/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:162360/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGa                  <  1:2394498/69‑1 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGAGCgt                  >  1:1121809/1‑68 (MQ=255)
                                              tATGTACGTGCTGCATCACGCCGATCAGCAGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGAGCgt                  >  1:1717443/1‑68 (MQ=255)
                                                  tACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGacac               <  1:2855779/68‑1 (MQ=255)
                                                    cGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTc            >  1:446842/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:2131095/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:717851/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:357867/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:354877/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:1091091/1‑69 (MQ=255)
                                                             tCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCt   >  1:219000/1‑69 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:652478/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:2143512/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:186689/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:1359722/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:143534/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:3193513/1‑68 (MQ=255)
                                                               aCGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCtg  >  1:1483654/1‑68 (MQ=255)
                                                                |                                                                  
AACATGCTGGCGTCTACAACCCGGAAGGGGTCGGTGGTACGCACGTTATGTACGTGCTGCATCACGCCGATCAGCCGGAGCTGTATCACGGTCTGCCGAAAGATCCGAAGATCGACACCTCGGTAAGCCTG  >  minE/936189‑936319

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