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 2,447,486 G→A 58.7% pseudogene (570/1647 nt) ilvG ← Mutation in protein compared to W3110: p.Glu327_Ilefs*223 Restoration of IlvG found in MG1655 (548 amino acids), fusion of N‑ter and C‑ter fragments ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,447,4860GA58.7% 60.0 / 127.5 167pseudogene (570/1647 nt)ilvGMutation in protein compared to W3110: p.Glu327_Ilefs*223 Restoration of IlvG found in MG1655 (548 amino acids), fusion of N‑ter and C‑ter fragments ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II
Reads supporting (aligned to +/- strand):  ref base G (32/37);  new base A (41/57);  total (73/94)
Fisher's exact test for biased strand distribution p-value = 6.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.94e-01

Only 100 of 180 total aligned reads displayed.

TGCGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACGGTGGTGAAC  >  minE/2447424‑2447543
                                                              |                                                         
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:2120458/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:3253499/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:141169/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:3379596/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:1549220/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:267757/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:274960/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGgcgcg                                                       <  1:2913539/67‑1 (MQ=255)
tgcGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCt                                                     <  1:614257/69‑1 (MQ=255)
    ccATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGc                                                  >  1:174269/1‑68 (MQ=255)
    ccATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGc                                                  >  1:910771/1‑68 (MQ=255)
    ccATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGc                                                  >  1:2131867/1‑68 (MQ=255)
    ccATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGc                                                  >  1:2811726/1‑68 (MQ=255)
    ccATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGc                                                  >  1:735690/1‑68 (MQ=255)
     cATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTc                                                <  1:1821118/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCt                                                     >  1:2871849/1‑60 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAAc                                             >  1:3306578/1‑68 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACt                                            >  1:3146068/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACt                                            >  1:1167764/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGAc                                             >  1:3144788/1‑68 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:348920/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:1896812/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:2070871/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:40904/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:983304/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:2241332/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:2246697/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:2436468/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:257765/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:278775/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:2958353/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:1620181/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:1313286/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:1296279/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:1289143/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:1223350/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:1486520/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:1117103/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            <  1:96522/69‑1 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:581177/1‑69 (MQ=255)
         cccACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACt                                            >  1:1873453/1‑69 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:3068942/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:1198574/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:1799879/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:1844807/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:410883/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:31199/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:52463/69‑1 (MQ=255)
             cGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCgg                                        <  1:1353645/69‑1 (MQ=255)
                 aCCGCCAACGTACAGCATCGTTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:1725651/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:978844/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:1891617/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:2582856/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:2538243/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:314970/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:2404970/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:3207282/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:331674/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:68770/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:1634423/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:1658251/1‑57 (MQ=255)
                 aCCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTc                                                >  1:2087573/1‑57 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:73947/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:721634/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:2470746/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:1009982/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:1179786/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:263371/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:2496031/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:1959682/69‑1 (MQ=255)
                          gTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGt                           <  1:2305186/69‑1 (MQ=255)
                             cAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCa                         >  1:1590409/1‑68 (MQ=255)
                             cAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCAc                        >  1:41481/1‑69 (MQ=255)
                             cAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCAc                        >  1:3174302/1‑69 (MQ=255)
                             cAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCAc                        >  1:1005111/1‑69 (MQ=255)
                                    ggTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCAtg                                    >  1:1379150/1‑50 (MQ=255)
                                    ggTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCAtg                                    >  1:505588/1‑50 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCaa             >  1:1046948/1‑69 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCaa             >  1:859587/1‑69 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:2323288/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:804708/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:74489/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:1513518/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:582538/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:1867540/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:3012504/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:1940074/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:232/69‑1 (MQ=255)
                                        tttGCGCTTTTGCCAGCATCTGACGCGCTTGCTCGACTTCGGCATGTGAGAAAGTCACTTCGTTTTCaa             <  1:3295315/69‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:1759134/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:2563811/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:1451266/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:1443027/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:2015076/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:2258368/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:1103331/68‑1 (MQ=255)
                                             gcTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACggt         <  1:3019533/68‑1 (MQ=255)
                                                    ccAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACGGTGGTGAAc  <  1:2846924/68‑1 (MQ=255)
                                                    ccAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACGGTGGTGAAc  <  1:943435/68‑1 (MQ=255)
                                                    ccAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACGGTGGTGAAc  <  1:2351657/68‑1 (MQ=255)
                                                              |                                                         
TGCGCCATACCCACGCCACCGCCAACGTACAGCATCGGTTTTTGCGCTTTTGCCAGCATCTGGCGCGCTTGCTCAACTTCGGCATGTGGGAAAGTCACTTCGTTTTCAACGGTGGTGAAC  >  minE/2447424‑2447543

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