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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,978,639 C→T 33.2% P539P (CCC→CCT)  slt → lytic murein transglycosylase, soluble

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,978,6390CT33.2% 67.9 / 43.4 84P539P (CCC→CCT) sltlytic murein transglycosylase, soluble
Reads supporting (aligned to +/- strand):  ref base C (22/34);  new base T (21/7);  total (43/41)
Fisher's exact test for biased strand distribution p-value = 2.59e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

GCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTACC  >  minE/2978574‑2978703
                                                                 |                                                                
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCg                                                                 >  1:2794197/1‑67 (MQ=255)
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGt                                                               >  1:1015336/1‑69 (MQ=255)
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGt                                                               <  1:1637539/69‑1 (MQ=255)
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGt                                                               >  1:1381408/1‑69 (MQ=255)
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGt                                                               >  1:2585391/1‑69 (MQ=255)
gCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGt                                                               <  1:848615/69‑1 (MQ=255)
    gCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTtata                                                           <  1:2883903/69‑1 (MQ=255)
    gCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTtata                                                           <  1:2111738/69‑1 (MQ=255)
    gCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTtata                                                           <  1:1209894/69‑1 (MQ=255)
    gCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTtata                                                           <  1:2407622/69‑1 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:3404797/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2721923/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2399396/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:3396002/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:521690/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:3265300/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2640317/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:3105631/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:627548/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2858394/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2647734/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1849184/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1543601/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:106198/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1103687/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1138020/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:2934989/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1229020/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1401669/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTtat                                                            >  1:1435590/1‑61 (MQ=255)
           gATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCTGGTta                                                             >  1:828931/1‑60 (MQ=255)
                   ttATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAAt                                            >  1:1683764/1‑69 (MQ=255)
                    tATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAAtt                                           >  1:208844/1‑69 (MQ=255)
                    tATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAAtt                                           >  1:897030/1‑69 (MQ=255)
                         cTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTgg                                      >  1:777849/1‑69 (MQ=255)
                         cTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTgg                                      >  1:196865/1‑69 (MQ=255)
                         cTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTgg                                      >  1:915417/1‑69 (MQ=255)
                         cTGGTACAGCGACACATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTgg                                      >  1:1037098/1‑69 (MQ=255)
                                 gCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGaa                              >  1:279172/1‑69 (MQ=255)
                                 gCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGaa                              >  1:1068788/1‑69 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:3256169/69‑1 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:3271710/69‑1 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:2947844/69‑1 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:2483319/69‑1 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:472657/69‑1 (MQ=255)
                                    aCCCATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:703382/69‑1 (MQ=255)
                                      ccATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         >  1:3291731/1‑69 (MQ=255)
                                       cATACGGTGAAGATGTTCTCTATTCCTGGTTATAGCAGCCCTGGGCAATTGCTGGATCCGGAAACg                           <  1:2611797/66‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:3345955/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:61981/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:848700/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:883549/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:1035659/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:1469360/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:2078204/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:2321685/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:1298607/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:2610297/69‑1 (MQ=255)
                                          aCGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTCGGCAATTGCTGGATCCGGAAACGAATATc                     <  1:92754/69‑1 (MQ=255)
                                           cGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGa                               >  1:3430971/1‑58 (MQ=255)
                                           cGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGa                               >  1:45346/1‑58 (MQ=255)
                                           cGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGa                               >  1:2854529/1‑58 (MQ=255)
                                           cGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGa                               >  1:614060/1‑58 (MQ=255)
                                               gAAGATTTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:1211625/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:1139944/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:2527046/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:1335733/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:817294/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:1976469/60‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:111753/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:1080303/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:916158/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:792639/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:594540/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:188816/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:2423104/69‑1 (MQ=255)
                                               gAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACAt                <  1:2774655/69‑1 (MQ=255)
                                                     gTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGaa                         <  1:495375/54‑1 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGtt     <  1:2142989/66‑1 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGtt     <  1:2782427/66‑1 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTAcc  >  1:252738/1‑69 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTAcc  >  1:3283744/1‑69 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTAcc  >  1:3265246/1‑69 (MQ=255)
                                                             ttCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTAcc  >  1:2818922/1‑69 (MQ=255)
                                                                 |                                                                
GCCAGCGGCTTGATGCAGATTATGCCTGGTACAGCGACCCATACGGTGAAGATGTTCTCTATTCCCGGTTATAGCAGTCCTGGGCAATTGCTGGATCCGGAAACGAATATCAACATTGGCACCAGTTACC  >  minE/2978574‑2978703

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