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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,519,938 A→G 29.2% E160E (GAA→GAG)  glpK → glycerol kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,519,9380AG29.2% 92.4 / 51.3 65E160E (GAA→GAG) glpKglycerol kinase
Reads supporting (aligned to +/- strand):  ref base A (25/21);  new base G (12/7);  total (37/28)
Fisher's exact test for biased strand distribution p-value = 5.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

TTTCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCATGTGACCGAT  >  W3110S.gb/3519868‑3520007
                                                                      |                                                                     
tttCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGaa                                                                       >  1:92424/1‑71 (MQ=255)
 ttCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAAt                                                                      >  1:2364685/1‑71 (MQ=255)
 ttCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAAt                                                                      >  1:1702635/1‑71 (MQ=255)
 ttCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTAGCGAGCGTGCACGTCGTGGTGAAt                                                                      >  1:3621360/1‑71 (MQ=255)
   cTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGGGAAtt                                                                     <  1:2352064/70‑1 (MQ=255)
         ccAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGc                                                                   <  1:2870640/66‑1 (MQ=255)
           aaaGTGAAGTGGATGCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGttt                                                              >  1:1499796/1‑69 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGaa                                                                       >  1:983919/1‑60 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGaa                                                                       >  1:1111731/1‑60 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGaa                                                                       >  1:1204191/1‑60 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGttt                                                              >  1:1148324/1‑69 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTT‑CTGttt                                                              >  1:1439840/1‑68 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGt                                                                >  1:3705649/1‑67 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTgg                                                            <  1:1481053/71‑1 (MQ=255)
           aaaGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTgg                                                            <  1:3412627/71‑1 (MQ=255)
                  agtgGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGtt                                                     <  1:2568535/71‑1 (MQ=255)
                  agtgGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGtt                                                     <  1:3914817/71‑1 (MQ=255)
                   gtgGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGtt                                                     >  1:1888965/1‑70 (MQ=255)
                    tgGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGa                                                   <  1:3605978/71‑1 (MQ=255)
                    tgGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGa                                                   <  1:2161271/71‑1 (MQ=255)
                      gATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATa                                                 <  1:2628180/71‑1 (MQ=255)
                      gATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATa                                                 >  1:1632006/1‑71 (MQ=255)
                      gATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATa                                                 >  1:140499/1‑71 (MQ=255)
                       aTCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATAc                                                <  1:924986/71‑1 (MQ=255)
                       aTCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATAc                                                <  1:205130/71‑1 (MQ=255)
                          cTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTg                                             <  1:2651477/71‑1 (MQ=255)
                          cTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTg                                             <  1:3760926/71‑1 (MQ=255)
                           tCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTg                                             <  1:2158544/70‑1 (MQ=255)
                              aCCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCtt                                         <  1:1404769/71‑1 (MQ=255)
                               ccATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTa                                        <  1:3511316/71‑1 (MQ=255)
                                cATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTAt                                       >  1:1879196/1‑71 (MQ=255)
                                 aTGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGa                                                   <  1:945827/58‑1 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGaa                                                                       >  1:393182/1‑35 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTg                                    >  1:49145/1‑70 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTg                                    >  1:1567819/1‑70 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTg                                    >  1:1119041/1‑70 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTa                                                          >  1:62447/1‑48 (MQ=255)
                                    tgGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTa                                                          >  1:2061353/1‑48 (MQ=255)
                                      gAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGaa                                 <  1:1911140/71‑1 (MQ=255)
                                        aGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGATGATACGTGGCTTATCTGGaaaa                               >  1:3666209/1‑71 (MQ=255)
                                         ggCTCTCGGGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACgg                                                       >  1:937048/1‑46 (MQ=255)
                                         ggCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAAt                              <  1:351982/71‑1 (MQ=255)
                                          gCTCTCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAAt                              >  1:2843255/1‑70 (MQ=255)
                                           ctctCGCGAGCGTGCACGTGGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGa                            >  1:3176819/1‑71 (MQ=255)
                                           ctctCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACTGTTGATACGTGGCTTATCTGGAAAATGa                            >  1:1129987/1‑71 (MQ=255)
                                           ctctCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGa                            >  1:105865/1‑71 (MQ=255)
                                           ctctCGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGa                            >  1:4052878/1‑71 (MQ=255)
                                           ctctCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGa                            >  1:264199/1‑71 (MQ=255)
                                              tcGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTa                                                          >  1:3560835/1‑38 (MQ=255)
                                              tcGCGAGCGTGCACGTCGTGGTGAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACt                          >  1:3668169/1‑70 (MQ=255)
                                               cgcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGtt                                                     <  1:3271761/42‑1 (MQ=255)
                                                gtgAGCGTGCACGTCGTGGTTAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTc                         <  1:3249302/67‑1 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGa                                                   >  1:2310470/1‑43 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGa                                                   >  1:1197428/1‑43 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGa                                                   >  1:1595560/1‑43 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTc                         <  1:1545066/69‑1 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAg                       >  1:874000/1‑71 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAg                       <  1:2741003/71‑1 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAg                       >  1:3339265/1‑71 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAg                       >  1:2930573/1‑71 (MQ=255)
                                                gcgAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAg                       >  1:2262936/1‑71 (MQ=255)
                                                 tgAGCGTGCACGTCGTGGTTAGTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTc                         <  1:3249306/67‑1 (MQ=255)
                                                   aGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGc                    <  1:1123251/71‑1 (MQ=255)
                                                      gTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGaaaa                               >  1:142628/1‑57 (MQ=255)
                                                         cACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTc              >  1:182660/1‑71 (MQ=255)
                                                           cgtcgtGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCa            <  1:976307/71‑1 (MQ=255)
                                                            gtcgtGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTc                         >  1:1091943/1‑57 (MQ=255)
                                                               gtggtgAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCa                        >  1:3919363/1‑55 (MQ=255)
                                                               gtggtgAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCAtgt         <  1:3169938/70‑1 (MQ=255)
                                                               gtggtgAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCAtgt         <  1:747366/70‑1 (MQ=255)
                                                                     aaTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCATGTGACCGAt  <  1:3318220/71‑1 (MQ=255)
                                                                     aaTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCATGTGACCGAt  <  1:107168/71‑1 (MQ=255)
                                                                     aaTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGACGTGTCCATGTGACCGAt  <  1:3692141/71‑1 (MQ=255)
                                                                      aTTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCATGTGACCGAt  <  1:90575/70‑1 (MQ=255)
                                                                      |                                                                     
TTTCTGGCACCAAAGTGAAGTGGATCCTCGACCATGTGGAAGGCTCTCGCGAGCGTGCACGTCGTGGTGAATTGCTGTTTGGTACGGTTGATACGTGGCTTATCTGGAAAATGACTCAGGGCCGTGTCCATGTGACCGAT  >  W3110S.gb/3519868‑3520007

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