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
A1 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,486,264 C→T P752P (CCG→CCA)  valS ← valyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,486,2640CT94.4% 214.0 / 2.6 71P752P (CCG→CCA) valSvalyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base C (2/2);  new base T (44/23);  total (46/25)
Fisher's exact test for biased strand distribution p-value = 6.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATCGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACCGCG  >  W3110S.gb/4486204‑4486323
                                                            |                                                           
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:979134/1‑69 (MQ=255)
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:1283108/1‑69 (MQ=255)
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:2264412/1‑69 (MQ=255)
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:3324578/1‑69 (MQ=255)
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:4036965/1‑69 (MQ=255)
aGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATgcgc                                                     >  1:41027/1‑69 (MQ=255)
   gATACCGCTAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgc                                                >  1:2153177/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAgg                                                 >  1:3458589/1‑70 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAgg                                                 >  1:4005181/1‑70 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgc                                                >  1:3679635/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgc                                                >  1:328821/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgc                                                >  1:2284725/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgc                                                >  1:471533/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATCGGATGCGCGAGgc                                                >  1:1557862/1‑71 (MQ=255)
   gATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATCGGATGCGCGAGgc                                                >  1:210668/1‑71 (MQ=255)
      aCCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgcg                                               >  1:1393089/1‑69 (MQ=255)
      aCCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGgcg                                               >  1:2076648/1‑69 (MQ=255)
       ccGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCgcag                                            <  1:3166929/71‑1 (MQ=255)
       ccGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCgcag                                            <  1:838669/71‑1 (MQ=255)
       ccGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCgcag                                            <  1:1389079/71‑1 (MQ=255)
       ccGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCgcag                                            <  1:1485491/71‑1 (MQ=255)
              gTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCt                                     >  1:2924500/1‑71 (MQ=255)
              gTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCt                                     >  1:2998830/1‑71 (MQ=255)
              gTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCt                                     >  1:2089186/1‑71 (MQ=255)
              gTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCt                                     >  1:1996717/1‑71 (MQ=255)
              gTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCt                                     >  1:82973/1‑71 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:3383244/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:1547733/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:2185411/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:122901/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:1607122/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:3241819/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:2584369/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:1787624/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:4135360/1‑67 (MQ=255)
                 cTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGAcc                                      >  1:2958941/1‑67 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:1145678/1‑71 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:712786/1‑71 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:1832935/1‑71 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:2540781/1‑71 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:2206494/1‑71 (MQ=255)
                   ttCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAg                                >  1:2004907/1‑71 (MQ=255)
                              ccAGATGGTTTCGGTTATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:2586946/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCTGCAGACCTTCCAGTACAGTCAc                       <  1:3197426/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:1669857/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:4069601/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:1894179/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:784261/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:1954523/69‑1 (MQ=255)
                              ccAGATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCAc                       <  1:809465/69‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCTCCAGCg                  <  1:527287/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:3505329/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:2364711/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:3126496/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:1844946/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:2652361/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:460588/71‑1 (MQ=255)
                                 gATGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:1034851/71‑1 (MQ=255)
                                   tGGTTTCGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTa                >  1:3547422/1‑71 (MQ=255)
                                     gTTTCGGTGATGAACGGAATGATCGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:1197121/67‑1 (MQ=255)
                                     gTTTCGGTGATGAACGGAATGATCGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:2704991/67‑1 (MQ=255)
                                         cGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCg           <  1:1634117/70‑1 (MQ=255)
                                         cGGTGATGAACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCg           <  1:2760646/70‑1 (MQ=255)
                                               tgaACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCg                  <  1:873816/57‑1 (MQ=255)
                                                gaACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgc   >  1:819187/1‑71 (MQ=255)
                                                gaACGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgc   >  1:3031765/1‑71 (MQ=255)
                                                 aaCGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgcg  >  1:170162/1‑71 (MQ=255)
                                                 aaCGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgcg  >  1:3913160/1‑71 (MQ=255)
                                                 aaCGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgcg  >  1:1961313/1‑71 (MQ=255)
                                                 aaCGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgcg  >  1:1606601/1‑71 (MQ=255)
                                                 aaCGGAATGATTGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACcgcg  >  1:2861827/1‑71 (MQ=255)
                                                            |                                                           
AGTGATACCGCAAAGTACTTTCACACGCTGCCAGATGGTTTCGGTGATGAACGGAATGATCGGATGCGCGAGGCGCAGCAGACCTTCCAGTACAGTCACCAGCGTATGGCGAGTACCGCG  >  W3110S.gb/4486204‑4486323

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