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 1,847,181 C→A 34.9% H312Q (CAC→CAA)  iap → aminopeptidase in alkaline phosphatase isozyme conversion

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,847,1810CA34.9% 130.8 / 83.7 120H312Q (CAC→CAA) iapaminopeptidase in alkaline phosphatase isozyme conversion
Reads supporting (aligned to +/- strand):  ref base C (53/25);  new base A (26/16);  total (79/41)
Fisher's exact test for biased strand distribution p-value = 5.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

Only 100 of 126 total aligned reads displayed.

CAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGTTATGCGGATAATGC  >  minE/1847116‑1847248
                                                                 |                                                                   
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:967756/69‑1 (MQ=255)
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:558057/69‑1 (MQ=255)
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:2188847/69‑1 (MQ=255)
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:1705044/69‑1 (MQ=255)
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:1465775/69‑1 (MQ=255)
cAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:2707557/69‑1 (MQ=255)
 aaCGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCaa                                                                  <  1:1549724/68‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTTCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1379946/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1244246/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:3120967/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1881844/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:2873423/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:144535/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1121742/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1471977/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1100448/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1515332/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAACAGCatat                                                             <  1:1887768/69‑1 (MQ=255)
     cgcAAAAACAGCCGCATTCCCTGCGGGAAATAGCTGGCATCACGTAAGACTGGATAATCAACAGCatat                                                             <  1:293795/69‑1 (MQ=255)
     cgcAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAcc                                                                    <  1:3065601/62‑1 (MQ=255)
     cgcAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAcc                                                                    <  1:810524/62‑1 (MQ=255)
     cgcAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAcc                                                                    <  1:1498847/62‑1 (MQ=255)
     cgcAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAcc                                                                    <  1:1498220/62‑1 (MQ=255)
       cAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTg                                                           <  1:2279696/69‑1 (MQ=255)
                 tGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGctct                                                 >  1:323879/1‑69 (MQ=255)
                  gCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCAcc                                                                    <  1:1770788/49‑1 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:1022419/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:128503/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:1719556/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:1096396/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:285036/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:2838386/1‑68 (MQ=255)
                     ttCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTcc                                              >  1:2784096/1‑68 (MQ=255)
                                 aaTAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGaa                                 >  1:1585392/1‑69 (MQ=255)
                                 aaTAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGaa                                 >  1:3123321/1‑69 (MQ=255)
                                     gCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAg                                                      >  1:1847969/1‑44 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:2187337/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:2280977/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:431848/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:200079/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:1791680/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:799681/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:318301/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:3417945/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:1422302/1‑69 (MQ=255)
                                           aTGACGTAAGACTGGATAATCACCAACATATTGAT‑AGGCTCTTCCTGGAAGAATAGAACGTCGCTGcc                       >  1:2773870/1‑68 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:505127/1‑69 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:1698651/1‑69 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:956246/1‑69 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:2927616/1‑69 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:3358850/1‑69 (MQ=255)
                                              aCGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTg                    >  1:360800/1‑69 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:357888/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:3430403/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:3353613/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:3296411/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2896468/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:3062606/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:3162631/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2970602/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2144691/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1653844/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:964718/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1726470/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1726814/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:673970/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1858509/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1898800/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2166947/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2290092/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2414164/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1364074/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1348644/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:1331315/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2630414/1‑67 (MQ=255)
                                                 tAAGACTGGATAATCAACAGCATATTGATAAGGCACTTCCTGGAAGAATAGAACGTCGCTGCCGTGat                  >  1:2654984/1‑67 (MQ=255)
                                                  aaGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                <  1:1620158/69‑1 (MQ=255)
                                                  aaGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                <  1:325826/69‑1 (MQ=255)
                                                    gACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                >  1:3319226/1‑67 (MQ=255)
                                                    gACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                >  1:279393/1‑67 (MQ=255)
                                                    gACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                >  1:3216789/1‑67 (MQ=255)
                                                    gACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                >  1:2468671/1‑67 (MQ=255)
                                                    gACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGt                >  1:2583032/1‑67 (MQ=255)
                                                                aCCAACATATTGATAAGTCTCTTCCTGGAAGAATAGAACGTc                             <  1:3429489/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:625817/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:504568/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:2380438/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:3269859/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:2875969/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:2779004/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:2418697/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:2208833/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:215652/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:1955027/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:1790628/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:1761554/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:1672652/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             <  1:1627867/42‑1 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTc                             >  1:1371312/1‑42 (MQ=255)
                                                                aCCAACATATTGATAAGGCTCTTCCTGG‑AGAATAGAACGTc                             <  1:1084185/41‑1 (MQ=255)
                                                                 |                                                                   
CAACGCGCAAAAACACCTGCCTTCCCGGCGGGAAATAGCTGGCATGACGTAAGACTGGATAATCACCAACATATTGATAAGGCTCTTCCTGGAAGAATAGAACGTCGCTGCCGTGACGTTATGCGGATAATGC  >  minE/1847116‑1847248

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