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
A8 F28 I1 R1 95 36.3 1231394 98.7% 1215385 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,243,195 T→C F6L (TTT→CTT)  emtA → lytic murein transglycosylase E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,243,1950TC97.4% 126.5 / ‑4.0 39F6L (TTT→CTT) emtAlytic murein transglycosylase E
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (19/19);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.51e-01

GTGAAACAGAGACATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGTTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGCCGGT  >  NC_000913/1243066‑1243320
                                                                                                                                 |                                                                                                                             
gTGAAACAGAGACATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCttttt                                                                                                                     <  2:442813/140‑1 (MQ=255)
    aaCAGAGACATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGAtt                                                                                                                 <  1:404464/140‑1 (MQ=255)
         agaCATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGtt                                                                                                            >  1:533343/1‑140 (MQ=255)
           aCATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGttat                                                                                                          >  1:179744/1‑140 (MQ=255)
                gCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCg                                                                                                     >  2:51860/1‑140 (MQ=255)
                gCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCg                                                                                                     >  2:247363/1‑140 (MQ=255)
                  aaTTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCggg                                                                                                   <  2:179744/140‑1 (MQ=255)
                  aaTTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCggg                                                                                                   <  1:51860/140‑1 (MQ=255)
                   aTTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGgt                                                                                                  >  1:109572/1‑140 (MQ=255)
                   aTTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGgt                                                                                                  >  1:455593/1‑140 (MQ=255)
                          gCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTCCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTtcat                                                                                           <  2:570315/140‑1 (MQ=255)
                               caacaGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAg                                                                                      <  2:331770/140‑1 (MQ=255)
                                 acaGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCa                                                                                    <  1:436634/140‑1 (MQ=255)
                                 acaGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCa                                                                                    <  2:533343/140‑1 (MQ=255)
                                  caGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCAt                                                                                   <  2:282777/140‑1 (MQ=255)
                                    gAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGa                                                                                 <  2:109572/140‑1 (MQ=255)
                                     aaaCGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGAc                                                                                <  1:564393/140‑1 (MQ=255)
                                              gTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAAc                                                                       <  1:247363/140‑1 (MQ=255)
                                              gTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTAATCAAAGCATGACTATACGAAc                                                                       <  2:455593/140‑1 (MQ=255)
                                               tataTCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAAcc                                                                      <  2:330065/140‑1 (MQ=255)
                                                         cGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGaa                                                            >  1:491860/1‑140 (MQ=255)
                                                         cGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGaa                                                            >  2:500133/1‑140 (MQ=255)
                                                         cGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATCGAGATGGCTTGCCTTTTTGATTGTTTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGaa                                                            >  2:478558/1‑140 (MQ=255)
                                                                               cTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGt                                      >  1:102521/1‑140 (MQ=255)
                                                                                  aaCGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCg                                   >  2:307301/1‑140 (MQ=255)
                                                                                    cGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGAt                                 <  2:583957/140‑1 (MQ=255)
                                                                                       cGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATTGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCa                              >  2:216314/1‑140 (MQ=255)
                                                                                         aTTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCa                              <  1:43567/138‑1 (MQ=255)
                                                                                         aTTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCa                              >  2:43567/1‑138 (MQ=255)
                                                                                         aTTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGt                            <  2:102521/140‑1 (MQ=255)
                                                                                               ggCTATAAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGc                      >  1:528480/1‑140 (MQ=255)
                                                                                                    taAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATa                 >  1:596340/1‑140 (MQ=255)
                                                                                                    taAGGATAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATa                 >  2:318641/1‑140 (MQ=255)
                                                                                                          tAGAAGAAGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAg           >  2:463906/1‑140 (MQ=255)
                                                                                                            gaagaaGTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGaa         >  1:119604/1‑140 (MQ=255)
                                                                                                              agaagTGAAATTGAGATGGTTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAg       >  2:514763/1‑140 (MQ=255)
                                                                                                               gaagTGAAATTGAGATGGCTTGCTTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGc      <  2:117672/140‑1 (MQ=255)
                                                                                                                  gTGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGCCgg   >  2:194492/1‑140 (MQ=255)
                                                                                                                   tGAAATTGAGATGGCTTGCTTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGCCGGt  <  1:500038/140‑1 (MQ=255)
                                                                                                                   tGAAATTGAGATGGCTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGCCGGt  <  1:307301/140‑1 (MQ=255)
                                                                                                                                 |                                                                                                                             
GTGAAACAGAGACATGGCAATTCCTTGCTGACAACAGAAACGAAATGTATATCATGCCGCTTAGGTGTGCCGTTGTCACCTCAACGGCGATTCCAGGCTATAAGGATAGAAGAAGTGAAATTGAGATGGTTTGCCTTTTTGATTGTGTTATTAGCGGGTTGTTCATCAAAGCATGACTATACGAACCCGCCGTGGAACGCGAAAGTTCCGGTGCAACGTGCGATGCAGTGGATGCCAATAAGCCAGAAAGCCGGT  >  NC_000913/1243066‑1243320

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A