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 F50 I1 R1 170 39.5 1266514 99.2% 1256381 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,594,432 A→G V350A (GTG→GCG)  livM ← branched‑chain amino acid ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,594,4320AG97.6% 131.8 / ‑3.8 41V350A (GTG→GCG) livMbranched‑chain amino acid ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (21/19);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.65e-01

ATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAACGG  >  NC_000913/3594288‑3594578
                                                                                                                                                |                                                                                                                                                  
atcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACg                                                                                                                                              <  2:344228/151‑1 (MQ=255)
 tcatcaGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGGCACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGcgca                                                                                                                                                  <  2:474694/146‑1 (MQ=255)
     caGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGAt                                                                                                                                         >  1:246612/1‑151 (MQ=255)
            aTCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCa                                                                                                                                   >  1:90998/1‑150 (MQ=255)
              cAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCaa                                                                                                                                  >  1:610861/1‑149 (MQ=255)
              cAAACCACCGAGCATTAACATGATGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCaaa                                                                                                                                 <  2:37183/150‑1 (MQ=255)
                     ccGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAgg                                                                                                                         <  2:15161/151‑1 (MQ=255)
                     ccGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAg                                                                                                                          <  1:558721/150‑1 (MQ=255)
                         gCATTAACATGCTGTATTCGTTGAAAACACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATAGCGAGCCGATACCGCCGAGCACCTCTATCGCCAGCGCAAACGCCGATTCGGCCAAGGTGAAGGATTc                                                                                                                     <  2:101827/151‑1 (MQ=255)
                            ttAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCgg                                                                                                                  >  1:630354/1‑151 (MQ=255)
                                    cTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACa                                                                                                           >  1:458110/1‑150 (MQ=255)
                                           cGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCt                                                                                                    <  1:311897/150‑1 (MQ=255)
                                              tGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGAc                                                                                                 <  1:500358/150‑1 (MQ=255)
                                               gAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGAcgc                                                                                               >  2:589662/1‑151 (MQ=255)
                                                 aaTCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACgcgc                                                                                             >  1:624530/1‑151 (MQ=255)
                                                           cAACTCGCGCGACACCACCAGCAAAATTGCCGCAAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCATAGGTGAAGCATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAg                                                                                    <  1:168809/150‑1 (MQ=255)
                                                            aaCTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCg                                                                                  >  2:161464/1‑151 (MQ=255)
                                                                cgcgcgACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTcc                                                                              >  1:316025/1‑151 (MQ=255)
                                                                 gcgcgACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCg                                                                             >  1:592338/1‑151 (MQ=255)
                                                                      acacCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCaaa                                                                        <  2:586158/151‑1 (MQ=255)
                                                                      acacCACCAGCAAAATTCCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCCCTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCaaa                                                                        <  2:253601/151‑1 (MQ=255)
                                                                         ccaccaGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAAcc                                                                     <  1:179619/151‑1 (MQ=255)
                                                                           accaGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCgg                                                                   >  2:591400/1‑151 (MQ=255)
                                                                                cAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAAc                                                              >  2:410506/1‑151 (MQ=255)
                                                                                   aaTTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAAcgcg                                                           <  2:610844/151‑1 (MQ=255)
                                                                                         cgccAGAATCCCCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACtt                                                     <  1:53188/151‑1 (MQ=255)
                                                                                            cAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATg                                                  <  2:457265/151‑1 (MQ=255)
                                                                                               aaTCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGt                                                <  2:134946/150‑1 (MQ=255)
                                                                                                aTCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTa                                               >  1:309554/1‑150 (MQ=255)
                                                                                                  cACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTaa                                              >  1:605595/1‑149 (MQ=255)
                                                                                                   aCCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAgg                                           >  2:166398/1‑151 (MQ=255)
                                                                                                          cttGCGAGCCCACACCGCCCAGCACCACTATCGCCAGCGCAAACGCCGCCTCGGCCAAGGTGAAGGATTCCGGGCTGACACAGCCCTCACGCCCCGCAAACAGCGCCCCGGCAAAACCCGCAAACGCCGCACTTACGGTAAAGCCAgcc                                      >  2:309157/2‑147 (MQ=255)
                                                                                                                       aCCGCCGAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGAcgc                       >  1:315659/1‑151 (MQ=255)
                                                                                                                          gccgAGCACCACTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCggg                    <  1:336640/151‑1 (MQ=255)
                                                                                                                                caccacTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAg              <  2:343397/151‑1 (MQ=255)
                                                                                                                                   cacTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGccc           >  2:138292/1‑151 (MQ=255)
                                                                                                                                    acTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGccc           >  1:474296/1‑150 (MQ=255)
                                                                                                                                    acTATCGCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCa          <  1:91900/151‑1 (MQ=255)
                                                                                                                                          gCCAGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAAc    >  1:618823/1‑151 (MQ=255)
                                                                                                                                            cAGCGCAAACGCCGATTCGGCAAAGGGGAAGGATTCCGGGCTAACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAACgg  >  1:76977/1‑151 (MQ=255)
                                                                                                                                             aGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAACgg  <  2:40777/150‑1 (MQ=255)
                                                                                                                                             aGCGCAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAACgg  >  1:40777/1‑150 (MQ=255)
                                                                                                                                                |                                                                                                                                                  
ATCATCAGCACCATCAAACCACCGAGCATTAACATGCTGTATTCGTTGAAATCACGCATCAACTCGCGCGACACCACCAGCAAAATTGCCGCCAGAATCACCGCAAATTGCGAGCCCATACCGCCGAGCACCACTATCGCCAGCACAAACGCCGATTCGGCAAAGGTGAAGGATTCCGGGCTGACAAAGCCCTGACGCGCCGCAAACAGCGTTCCGGCAAAACCGGCAAACGCGGCACTTATGGTAAAGGCAGTCAGCTTGATACGACGCGGGCTTAAGCCCAGCGAACGG  >  NC_000913/3594288‑3594578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A