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 1,463,780 G→A 32.4% G139G (GGC→GGT)  yfaA ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,463,7800GA32.4% 74.6 / 42.4 86G139G (GGC→GGT) yfaAhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (29/29);  new base A (12/16);  total (41/45)
Fisher's exact test for biased strand distribution p-value = 6.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-01

CAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCT  >  minE/1463714‑1463846
                                                                  |                                                                  
caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                                                  >  1:633476/1‑69 (MQ=255)
caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                                                  >  1:2033875/1‑69 (MQ=255)
caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                                                  >  1:1765460/1‑69 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:2963538/68‑2 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:2164166/68‑2 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:2392625/68‑2 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:1156007/68‑2 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:3096842/68‑2 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:1456644/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:780786/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:1952337/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:2154192/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:1452808/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:14162/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:3118967/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:2532600/68‑1 (MQ=255)
              gcagTTTGCTTAAACCACTGCGCTGGATAAGCAACATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:815617/68‑1 (MQ=255)
               cagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                                                     <  1:2198142/67‑1 (MQ=255)
                    tGCTTAGACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:442337/1‑53 (MQ=255)
                    tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAgcg                                              >  1:160417/1‑69 (MQ=255)
                    tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAgcg                                              >  1:68003/1‑69 (MQ=255)
                    tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTACCACAgcg                                              >  1:2358785/1‑69 (MQ=255)
                    tGCTTAAACCACTGCGCTGGATAAGTACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1385678/1‑53 (MQ=38)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTg                                                               >  1:1228194/1‑52 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:2943519/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1992293/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:3022761/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:2642370/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:331469/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1793206/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1311920/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1479937/1‑53 (MQ=39)
                    tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                                              >  1:1314167/1‑53 (MQ=39)
                            ccACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                                                     <  1:1563573/54‑2 (MQ=255)
                             cACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcg                                     >  1:834803/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:334675/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:1698007/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:1602883/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:1177003/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:2278212/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:1426978/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:2297112/1‑69 (MQ=255)
                              aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc                                    >  1:911224/1‑69 (MQ=255)
                                    cTGTATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:398018/69‑1 (MQ=255)
                                    cTGGATCAGCACCATATAATGTGAAAGATGGCCTTTTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:927668/69‑1 (MQ=255)
                                    cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:2261036/69‑1 (MQ=255)
                                    cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:2397379/69‑1 (MQ=255)
                                    cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:2465667/69‑1 (MQ=255)
                                    cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:95702/69‑1 (MQ=255)
                                     tGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:2586434/68‑1 (MQ=255)
                                     tGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg                              <  1:1868077/68‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:1185809/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:1808912/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:2419568/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:2398577/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:3369455/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:347755/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:2257489/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:495510/69‑1 (MQ=255)
                                              aCCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGt                    <  1:1766903/69‑1 (MQ=255)
                                                    taATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACg                >  1:1061346/1‑67 (MQ=255)
                                                    taATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACg                >  1:1046407/1‑67 (MQ=255)
                                                    taATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACg                >  1:1817269/1‑67 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:998762/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:1114821/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:2985336/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:2821835/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:2777924/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:1778681/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:795476/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:768291/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:1829248/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:2287247/37‑1 (MQ=255)
                                                           aaaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:466078/37‑1 (MQ=255)
                                                            aaGATGGCCTTGTTTATCGTGCCACAGCGctgcctg                                       <  1:234720/36‑1 (MQ=255)
                                                             aGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTa     >  1:2241705/1‑69 (MQ=255)
                                                             aGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTa     >  1:835925/1‑69 (MQ=255)
                                                             aGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTa     >  1:2350888/1‑69 (MQ=255)
                                                             aGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTa     >  1:254377/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATc   >  1:3098908/1‑68 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:1786410/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:272240/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:1313187/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:1308733/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2868081/1‑69 (MQ=255)
                                                                tGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2924440/1‑69 (MQ=255)
                                                                 ggCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2922999/1‑68 (MQ=255)
                                                                 ggCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2127115/1‑68 (MQ=255)
                                                                 ggCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:375801/1‑68 (MQ=255)
                                                                 ggCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2736526/1‑68 (MQ=255)
                                                                 ggCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCt  >  1:2898697/1‑68 (MQ=255)
                                                                  |                                                                  
CAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTGATCTAAGAGTGACGAAAAGAGCTTATCT  >  minE/1463714‑1463846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A