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
A12 F204 I1 R1 117 93.2 4682243 93.4% 4373214 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,594,073 G→T T45N (ACC→AAC)  livG ← branched‑chain amino acid ABC transporter ATPase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,594,0730GT94.7% 192.1 / 3.2 58T45N (ACC→AAC) livGbranched‑chain amino acid ABC transporter ATPase
Reads supporting (aligned to +/- strand):  ref base G (3/0);  new base T (32/22);  total (36/22)
Fisher's exact test for biased strand distribution p-value = 2.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-01

AATTTGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCG  >  NC_000913/3593976‑3594167
                                                                                                 |                                                                                              
aaTTTGCTGCCACGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGttt                                                                                              <  2:925655/100‑1 (MQ=255)
  tttGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTtttt                                                                                            >  1:67407/1‑100 (MQ=255)
       tgcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCgg                                                                                       <  1:1954938/100‑1 (MQ=255)
        gcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGc                                                                                      <  2:2178503/100‑1 (MQ=255)
             ggTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGt                                                                                 >  1:2311259/1‑100 (MQ=255)
             ggTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGt                                                                                 >  1:483083/1‑100 (MQ=255)
                  aCCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAggg                                                                            >  2:1837246/1‑100 (MQ=255)
                       ccAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGAt                                                                       >  1:2249257/1‑100 (MQ=255)
                        cAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGAtt                                                                      <  1:1974058/100‑1 (MQ=255)
                           gTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAAc                                                                   <  1:982927/100‑1 (MQ=255)
                            tGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACg                                                                  <  1:378702/100‑1 (MQ=255)
                            tGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACg                                                                  <  1:301234/100‑1 (MQ=255)
                             gCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACga                                                                 >  1:2252706/1‑100 (MQ=255)
                               tGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACgaga                                                               >  2:2266737/1‑100 (MQ=255)
                                gATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGAc                                                              >  2:2191637/1‑100 (MQ=255)
                                gATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGAc                                                              >  2:1941469/1‑100 (MQ=255)
                                gATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGAc                                                              >  2:169566/1‑100 (MQ=255)
                                gATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGAc                                                              >  1:2154947/1‑100 (MQ=255)
                                    gcgcAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGAtc                                                          >  1:2114958/1‑100 (MQ=255)
                                        aGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCt                                                      <  1:702665/100‑1 (MQ=255)
                                         gTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTg                                                     >  1:440473/1‑100 (MQ=255)
                                            aaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCgg                                                  <  2:597384/100‑1 (MQ=255)
                                            aaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCgg                                                  >  1:908516/1‑100 (MQ=255)
                                              aTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGt                                                <  1:464747/100‑1 (MQ=255)
                                                  tGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAg                                            >  2:630942/1‑100 (MQ=255)
                                                   gccgccGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTCCGGGTACGGt                                           >  1:2040146/1‑100 (MQ=255)
                                                     cgccgGTGGGTTTGTAGATTCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGGACAGTTc                                         >  2:2183568/1‑100 (MQ=255)
                                                     cgccgGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTc                                         >  1:1182284/1‑100 (MQ=255)
                                                         ggTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGa                                     >  2:287157/1‑100 (MQ=255)
                                                          gTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGAt                                    <  1:2266745/100‑1 (MQ=255)
                                                            gggTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTg                                  >  2:1465425/1‑100 (MQ=255)
                                                             ggTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGa                                 <  2:2154940/100‑1 (MQ=255)
                                                              gTTTGTAGAATCCGGTCAGACAGTTAAAATCCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGa                                 <  1:115527/99‑1 (MQ=255)
                                                              gTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGAc                                >  2:1900753/1‑100 (MQ=255)
                                                               tttGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACg                               <  1:1158567/100‑1 (MQ=255)
                                                                 tGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgtt                             >  1:503940/1‑100 (MQ=255)
                                                                  gTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgttg                            <  1:1941476/100‑1 (MQ=255)
                                                                   tAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgttgt                           <  2:51780/100‑1 (MQ=255)
                                                                     gAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTc                         <  1:1465429/100‑1 (MQ=255)
                                                                     gAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTc                         >  1:1322883/1‑100 (MQ=255)
                                                                       aTCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCAc                       >  2:1178388/1‑100 (MQ=255)
                                                                       aTCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCAc                       >  1:690982/1‑100 (MQ=255)
                                                                       aTCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGACCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCAc                       >  1:1342187/1‑100 (MQ=255)
                                                                          cGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGc                    >  1:992466/1‑100 (MQ=255)
                                                                          cGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGc                    >  2:1331232/1‑100 (MQ=255)
                                                                           ggTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGcc                   >  1:1923832/1‑100 (MQ=255)
                                                                            gTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGcc                   <  2:67405/99‑1 (MQ=255)
                                                                             tCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCcag                 <  2:503938/100‑1 (MQ=255)
                                                                               aGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCcagca               <  2:2311250/100‑1 (MQ=255)
                                                                               aGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCcagca               <  1:169568/100‑1 (MQ=255)
                                                                                 aCAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAgg             >  1:1472434/1‑100 (MQ=255)
                                                                                  cAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGCCGCTCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCcagca               >  1:1151124/1‑97 (MQ=255)
                                                                                  cAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgc            >  2:67686/1‑100 (MQ=255)
                                                                                   aGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgcc           >  2:391319/1‑100 (MQ=255)
                                                                                    gTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccg          >  2:830344/1‑100 (MQ=255)
                                                                                    gTTAAAAACCGTGATTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccg          >  1:1571192/1‑100 (MQ=255)
                                                                                       aaaaaCCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGccgccg       <  1:242103/100‑1 (MQ=255)
                                                                                       aaaaaCCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGccgccg       >  1:1409528/1‑100 (MQ=255)
                                                                                            ccGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAgcg  <  1:1367986/100‑1 (MQ=255)
                                                                                                 |                                                                                              
AATTTGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCG  >  NC_000913/3593976‑3594167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A