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 2,794,102 G→A L398L (TTG→TTA)  gabP → gamma‑aminobutyrate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,794,1020GA84.4% 227.8 / 33.2 90L398L (TTG→TTA) gabPgamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand):  ref base G (0/14);  new base A (39/37);  total (39/51)
Fisher's exact test for biased strand distribution p-value = 1.91e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

TAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGT  >  W3110S.gb/2794035‑2794167
                                                                   |                                                                 
taGTCATCGCCGTTTCACAGTTGCGGATGCGCGAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 <  1:936107/70‑1 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:505939/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:2252615/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:2449934/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:2501246/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:2554488/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:1819149/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:3297950/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:391895/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:570028/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:1497102/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:733160/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 <  1:82580/70‑1 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:827057/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:1182614/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 <  1:1141005/70‑1 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:111051/1‑70 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCCGCGAGCAGAAGGAAGCGAAATTCGCTTACg                                                                 >  1:563833/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:1103146/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:770474/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:3223878/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:2533004/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:2422509/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:231393/1‑70 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       <  1:2241975/70‑1 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtc                                                       >  1:1805361/1‑69 (MQ=255)
          cGTTTCACAGTTGCGGATGCGCAAAATTCTGCAAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       >  1:2035920/1‑70 (MQ=255)
               cacaGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATcc                                                  <  1:2672905/70‑1 (MQ=255)
               cacaGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATcc                                                  <  1:3284242/70‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:1966560/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:2711196/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:2937997/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:1841119/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:3042135/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:3370357/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:3464977/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:1502060/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:149902/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:599413/71‑1 (MQ=255)
                  aGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:82538/71‑1 (MQ=255)
                   gTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTgg                                              <  1:2990813/70‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGcc                                                                 <  1:1014531/50‑2 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCg                                                                 <  1:2409065/50‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCg                                                                 <  1:2859107/50‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCg                                                                 <  1:2878719/50‑1 (MQ=255)
                     tGCGGATGCGCAAAATTCTGCTAGCAGAAGGAAGCGAAATTCGCTTGCg                                                                 <  1:3386198/49‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCa                                          <  1:2181630/70‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCa                                          <  1:4087608/70‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCa                                          <  1:1830844/70‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCa                                          <  1:2651810/70‑1 (MQ=255)
                            gcgcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCtt                                                       <  1:1716102/52‑1 (MQ=255)
                             cgcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCa                                          <  1:3668835/64‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:2117724/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:2086363/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:524018/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:1401370/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:4041808/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:2025283/71‑1 (MQ=255)
                              gcAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:92787/71‑1 (MQ=255)
                               cAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:1823012/70‑1 (MQ=255)
                                aaaaTTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  <  1:209946/69‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:2519412/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:588953/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:574334/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:548775/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:817303/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:426498/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:3235925/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:3907660/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:3678449/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:1954770/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:3365780/50‑1 (MQ=255)
                                                            ttCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:3428670/50‑1 (MQ=255)
                                                             tCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  >  1:3149354/1‑40 (MQ=255)
                                                             tCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  >  1:3408948/1‑40 (MQ=255)
                                                             tCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTa                                  >  1:2027160/1‑40 (MQ=255)
                                                             tCGCTTAAGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc                         <  1:2500861/49‑1 (MQ=39)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:1253198/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:2787262/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:2817266/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:269644/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:602969/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:1891828/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:169/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:3911963/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:3793091/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt                       >  1:3629284/1‑50 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAg   >  1:543962/1‑70 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGt  >  1:1299639/1‑71 (MQ=255)
                                                              cGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGt  >  1:1211683/1‑71 (MQ=255)
                                                                   |                                                                 
TAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGT  >  W3110S.gb/2794035‑2794167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A