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
A1 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,397,191 A→G 78.3% F174S (TTC→TCC)  nuoM ← NADH:ubiquinone oxidoreductase, membrane subunit M

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,397,1910AG78.3% 176.7 / 42.8 83F174S (TTC→TCC) nuoMNADH:ubiquinone oxidoreductase, membrane subunit M
Reads supporting (aligned to +/- strand):  ref base A (10/8);  new base G (32/32);  total (42/41)
Fisher's exact test for biased strand distribution p-value = 7.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

ACAAAAACCAGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAGGA  >  W3110S.gb/2397128‑2397257
                                                               |                                                                  
aCAAAAACCAGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTg                                                               <  1:1024519/69‑1 (MQ=255)
         aGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGt                                                    <  1:2596110/71‑1 (MQ=255)
         aGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGt                                                    <  1:3584516/71‑1 (MQ=255)
         aGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGt                                                    <  1:2801192/71‑1 (MQ=255)
         aGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGt                                                    <  1:736354/71‑1 (MQ=255)
         aGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGt                                                    <  1:1749111/71‑1 (MQ=255)
            gcCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGa                                                  <  1:2665311/70‑1 (MQ=255)
                     gCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGttt                                         <  1:149838/70‑1 (MQ=255)
                     gCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:1563396/71‑1 (MQ=255)
                     gCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:3135271/71‑1 (MQ=255)
                     gCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:3139486/71‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTgccgcc                                                      <  1:2475273/53‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTgccgcc                                                      <  1:638089/53‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTg                                                   <  1:1134612/56‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTg                                                   <  1:1209442/56‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGa                                                  <  1:2530752/57‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGa                                                  <  1:2059411/57‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGa                                                  <  1:3441341/57‑1 (MQ=255)
                         tCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGa                                                  <  1:2385676/57‑1 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGt                                   >  1:2521704/1‑70 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGt                                   >  1:3704204/1‑70 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGt                                   >  1:3530542/1‑70 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGAt                                                 >  1:889501/1‑56 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATa                                                >  1:2011/1‑57 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATa                                                >  1:3085000/1‑57 (MQ=255)
                           aaCATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATa                                                >  1:2638119/1‑57 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTg                                                   <  1:759079/50‑1 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTg                                                   <  1:3330502/50‑1 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:3073693/61‑1 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:635039/61‑1 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGtttt                                        <  1:2739595/61‑1 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCagag                              >  1:775484/1‑71 (MQ=255)
                               tCACCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCagag                              >  1:548650/1‑71 (MQ=255)
                                 aCCAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATAAGCGTTTTACCGTCAGAgg                             <  1:2080919/70‑1 (MQ=255)
                                  ccAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAgg                             <  1:3207882/69‑1 (MQ=255)
                                   cAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:776773/71‑1 (MQ=255)
                                   cAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:2545578/71‑1 (MQ=255)
                                   cAGGCCACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:2533585/71‑1 (MQ=255)
                                       ccACTCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATg                      >  1:2998163/1‑71 (MQ=255)
                                        cACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGc                     >  1:3195849/1‑71 (MQ=255)
                                        cACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGc                     >  1:2011063/1‑71 (MQ=255)
                                           tCGCCTGGGTGTAAATGAATGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:418264/63‑1 (MQ=255)
                                           tCGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAgg                             <  1:1652372/60‑1 (MQ=255)
                                            cGCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGcccc                  >  1:2464838/1‑70 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTTCCGTCAGAGGCTTTa                        >  1:3413825/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:2938530/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:2276739/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:479621/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:2086598/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:1667176/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:3092454/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:3130919/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:792430/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:815030/1‑63 (MQ=255)
                                             gCCTGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGATTTa                        >  1:2633790/1‑63 (MQ=255)
                                              ccTGGGTGTAAATGAAGTACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:963818/60‑1 (MQ=255)
                                              ccTGGGTGTAAATCAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:1899365/60‑1 (MQ=255)
                                                tGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:324151/1‑60 (MQ=255)
                                                tGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:298648/1‑60 (MQ=255)
                                                tGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:2446268/1‑60 (MQ=255)
                                                tGGGTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:624675/1‑60 (MQ=255)
                                                 gggTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTaa                                      >  1:2754027/1‑44 (MQ=255)
                                                 gggTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTAc                                      >  1:1532932/1‑45 (MQ=255)
                                                 gggTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTAc                                      >  1:2550354/1‑45 (MQ=255)
                                                  ggTGTAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAg             <  1:1399481/69‑1 (MQ=255)
                                                    tgtAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCg         <  1:1832081/71‑1 (MQ=255)
                                                     gtAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCg         <  1:123277/70‑1 (MQ=255)
                                                     gtAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCg         <  1:748492/70‑1 (MQ=255)
                                                      tAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCtt                          <  1:1731996/52‑1 (MQ=255)
                                                      tAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCcaca              <  1:1056388/64‑1 (MQ=255)
                                                      tAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCcaca              <  1:2033115/64‑1 (MQ=255)
                                                      tAAATGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCcaca              <  1:3054596/64‑1 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAgg                             >  1:29703/1‑47 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGt            >  1:215429/1‑64 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGt            >  1:2518170/1‑64 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGAt       >  1:1785856/1‑69 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGAt       >  1:1744717/1‑69 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGAt       >  1:3568778/1‑69 (MQ=255)
                                                        aaTGAAGGACTTGGTTGCCGACGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGt            >  1:3187040/1‑64 (MQ=255)
                                                        aaTGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTa                        >  1:913600/1‑52 (MQ=255)
                                                          tGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAg    >  1:74034/1‑70 (MQ=255)
                                                          tGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAg    >  1:3668046/1‑70 (MQ=255)
                                                          tGAAGGACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAg    >  1:1071917/1‑70 (MQ=255)
                                                            aaggaCTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAGGa  <  1:3158492/70‑1 (MQ=255)
                                                               |                                                                  
ACAAAAACCAGCGCCAGGATGGCAATCAACATCACCAGGCCACTCGCCTGGGTGTAAATGAAGAACTTGGTTGCCGCCGTGATACGCGTTTTACCGTCAGAGGCTTTATGCCCCCACAGTGCGATCAGGA  >  W3110S.gb/2397128‑2397257

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