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
A12 F1 I1 R1 760 58.2 3022526 90.8% 2744453 102.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,606,094 (G)8→9 noncoding (72/87 nt) leuV ← tRNA‑Leu

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,606,0861.G91.5% 148.4 / 5.9 47noncoding (80/87 nt)leuVtRNA‑Leu
Reads supporting (aligned to +/- strand):  ref base . (1/3);  new base G (22/21);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 6.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

CCATCGTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑GGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG  >  NC_000913/4605978‑4606208
                                                                                                               |                                                                                                                           
ccATCGTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGTATCAGGGATGAAAAATCAAGGAAGTAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑g                                                                                                                            >  1:921934/1‑110 (MQ=255)
ccATCGTGCCTGGCACTTATTGCTGGCATCAAGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑g                                                                                                                            <  2:921934/110‑1 (MQ=255)
   tCGTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑ggggggggg                                                                                                                    >  1:1088484/1‑114 (MQ=255)
   tCGTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑ggggggggg                                                                                                                    <  2:1088484/115‑2 (MQ=255)
     gTGCCTGGCACTTATTGCTGGCATCATTCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGATGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑GGGGGGGGTACTTGAAcccc                                                                                                         <  1:586438/124‑1 (MQ=255)
     gTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAAcccc                                                                                                         >  2:586438/1‑124 (MQ=255)
      tGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTa                                                                                               >  2:809337/1‑133 (MQ=255)
      tGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTa                                                                                               <  1:809337/133‑1 (MQ=255)
            gCACTTATTGCTGGCATCATGCTGATGATGATGAATTTGAATCAGTGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑ggggg                                                                                                                        >  2:869609/1‑102 (MQ=255)
            gCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAaca                                                                                   >  2:460385/1‑139 (MQ=255)
            gCACTTATTGCTGGCATCATGCTGATGATAAGGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑ggggg                                                                                                                        <  1:869609/102‑1 (MQ=255)
                 tATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGa                                                                              >  2:199388/1‑139 (MQ=255)
                  aTTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       <  2:1369489/113‑1 (MQ=255)
                  aTTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       >  1:1369489/1‑113 (MQ=255)
                   ttGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       >  1:1339526/1‑112 (MQ=255)
                   ttGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       <  2:1339526/112‑1 (MQ=255)
                            tcatGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCAc                                                                                                      <  2:1065461/104‑1 (MQ=255)
                            tcatGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCAc                                                                                                      >  1:1065461/1‑104 (MQ=255)
                               tGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTa                                                                <  1:938730/139‑1 (MQ=255)
                                 cTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTAcc                                                              <  1:1024356/139‑1 (MQ=255)
                                         aaTGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       >  2:355314/1‑90 (MQ=255)
                                         aaTGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       <  1:355314/90‑1 (MQ=255)
                                         aaTGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc                                                      >  1:312046/1‑139 (MQ=255)
                                            gAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCAc                                                   <  1:199388/139‑1 (MQ=255)
                                                 tGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAAcccc                                                                                                         <  1:1220865/80‑1 (MQ=255)
                                                 tGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAAcccc                                                                                                         >  2:1220865/1‑80 (MQ=255)
                                                  taaTCAGGGAATAAAAATCAAGGAAGAAACAAAAAAGGAAGTAAAGATAATTGGTGCCAGG‑GGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCg                                              <  2:918198/138‑1 (MQ=18)
                                                   aaTCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGca                                            >  2:412044/1‑139 (MQ=255)
                                                     tCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGcaca                                          <  1:460385/139‑1 (MQ=255)
                                                     tCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGcaca                                          <  1:412044/139‑1 (MQ=255)
                                                       aGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTaa                                                                                     >  2:1099791/1‑94 (MQ=255)
                                                       aGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTaa                                                                                     <  1:1099791/94‑1 (MQ=255)
                                                             gAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       <  1:209728/70‑1 (MQ=255)
                                                             gAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCa                                                                                                       >  2:209728/1‑70 (MQ=255)
                                                                   tCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTaa                                                                                     >  2:1290959/1‑82 (MQ=255)
                                                                   tCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTaa                                                                                     <  1:1290959/82‑1 (MQ=255)
                                                                         aagaaACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑GGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGcaca                                          <  2:365890/118‑1 (MQ=255)
                                                                         aagaaACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑GGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGcaca                                          >  1:365890/1‑118 (MQ=255)
                                                                             aaCAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAg                                                                                             >  2:313375/1‑64 (MQ=255)
                                                                             aaCAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAg                                                                                             <  1:313375/64‑1 (MQ=255)
                                                                             aaCAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCa                                                             >  1:1231483/1‑96 (MQ=255)
                                                                             aaCAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCa                                                             <  2:1231483/96‑1 (MQ=255)
                                                                              aCAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                 <  2:312046/139‑1 (MQ=255)
                                                                                     aGGAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTAC‑TTTTTTGATATCGCCTCGTTTg         >  1:1258141/1‑139 (MQ=255)
                                                                                      ggAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc                                                      >  2:455052/1‑94 (MQ=255)
                                                                                      ggAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc                                                      <  1:455052/94‑1 (MQ=255)
                                                                                       gAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAAcccc                                                                                                         >  1:88695/1‑42 (MQ=21)
                                                                                       gAAGTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAAcccc                                                                                                         <  2:88695/42‑1 (MQ=21)
                                                                                          gTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCa                                                             <  1:1328571/83‑1 (MQ=255)
                                                                                          gTAAAGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCa                                                             >  2:1328571/1‑83 (MQ=255)
                                                                                             aaGATAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg  >  1:596582/1‑139 (MQ=255)
                                                                                                 tAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                  <  2:927818/119‑1 (MQ=255)
                                                                                                 tAATTGGTGC‑‑GAGGGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                  >  1:927818/1‑119 (MQ=255)
                                                                                                               |                                                                                                                           
CCATCGTGCCTGGCACTTATTGCTGGCATCATGCTGATGATAATGAATTTGAATCAGGGATGAAAAATCAAGGAAGAAACAAGAAAGGAAGTAAAGATAATTGGTGC‑‑GA‑GGGGGGGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG  >  NC_000913/4605978‑4606208

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A