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 F17 I0 R1 71 95.7 2922988 91.7% 2680379 65.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 782,109 T→C 66.3% Q167R (CAG→CGG)  hlyE ← hemolysin E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE782,1090TC66.3% 209.3 / 177.4 175Q167R (CAG→CGG) hlyEhemolysin E
Reads supporting (aligned to +/- strand):  ref base T (15/44);  new base C (39/77);  total (54/121)
Fisher's exact test for biased strand distribution p-value = 3.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.24e-01

Only 100 of 175 total aligned reads displayed.

GACACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAA  >  minE/782054‑782158
                                                       |                                                 
gacACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGG‑AATAGCTGCtttt                                   <  1:769441/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:2245114/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:154883/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:1499764/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:2309536/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:2285645/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:1258718/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:1241252/71‑1 (MQ=255)
 acacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:330564/71‑1 (MQ=255)
  cacCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCtttt                                   <  1:1666758/70‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTAGCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:1977624/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2193247/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:1507483/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:173218/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2125574/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:1614260/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2419867/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2450281/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:1964598/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2585017/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:153898/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:259606/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2687344/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:275427/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:1292247/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:44355/71‑1 (MQ=255)
                ccGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:596007/71‑1 (MQ=255)
                           ttccttccTGATTTTATCTACCTGTGACCGCAAATAGCTGCTTTTTTCTGAAAAATCAtt                    <  1:2764091/60‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:1009904/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:2617601/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:2916286/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:2144570/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:783830/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:1913223/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:1675332/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAAt                        >  1:1941313/1‑50 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2860909/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2353134/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2462667/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2499323/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:156447/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1467365/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1423010/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1346318/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2710679/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:372212/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1182970/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:531520/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:631790/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1009284/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:807028/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:848404/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:996597/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2326637/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2055003/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2075666/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1855110/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1892729/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2222066/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1764796/70‑1 (MQ=255)
                                 cctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTATGaaa                           >  1:2177926/1‑47 (MQ=255)
                                  ctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:489902/69‑1 (MQ=255)
                                  ctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1220376/69‑1 (MQ=255)
                                  ctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1092121/69‑1 (MQ=255)
                                  ctGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATT‑GTTAACTGGCTATCt    <  1:1133301/68‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:928862/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:734541/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:30122/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2879964/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:805822/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:2163319/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1967848/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:196145/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1408427/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1816227/65‑1 (MQ=255)
                                      ttttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCt    <  1:1642952/65‑1 (MQ=255)
                                        ttATCTACCTGTGCCCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:535582/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGATATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1597232/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1951886/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2345940/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2026408/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:661473/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:986598/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:917846/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:923345/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:462809/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:444236/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:390240/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:334321/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1194766/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2905714/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1827127/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2783158/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1400199/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2719890/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2229800/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2522606/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2478014/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:1583659/1‑65 (MQ=255)
                                        ttATCTACCTGTGACCGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTaa  >  1:2371289/1‑65 (MQ=255)
                                                       |                                                 
GACACCGGCTGCGGCACCGGCATATGCTTCCTTCCTGATTTTATCTACCTGTGACTGGAAATAGCTGCTTTTTTCTGAAAAATCATTGGTTAACTGGCTATCTAA  >  minE/782054‑782158

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