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 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,088,257 T→C intergenic (+397/‑27) metK → / → galP S‑adenosylmethionine synthetase/D‑galactose transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,088,2570TC98.0% 171.0 / ‑6.6 49intergenic (+397/‑27)metK/galPS‑adenosylmethionine synthetase/D‑galactose transporter
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (24/24);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTG  >  NC_000913/3088126‑3088392
                                                                                                                                   |                                                                                                                                       
tCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATTTTAGTGTAAGCGATTACACTGATGTGATTTGCTTAACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAAt                                                                                                                                  <  2:325386/139‑1 (MQ=255)
tCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAAt                                                                                                                                  <  1:679196/139‑1 (MQ=255)
    tgatgaTATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAAcc                                                                                                                              >  1:2953/1‑139 (MQ=255)
    tgatgaTATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAAcc                                                                                                                              <  2:199936/139‑1 (MQ=255)
     gatgatATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCa                                                                                                                             <  2:2953/139‑1 (MQ=255)
         atatAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATAtt                                                                                                                         <  1:736261/139‑1 (MQ=255)
          tataACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAATTAACCATATTg                                                                                                                        >  1:1300007/1‑139 (MQ=255)
             aaCTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAg                                                                                                                     <  1:140392/139‑1 (MQ=255)
               cTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAggg                                                                                                                   >  2:309645/1‑139 (MQ=255)
               cTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAggg                                                                                                                   >  2:242019/1‑139 (MQ=255)
                 cAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGca                                                                                                                 >  1:941621/1‑139 (MQ=255)
                            aTGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACTATATTGGAGGGCATCATGCCTGAc                                                                                                      >  2:983182/1‑139 (MQ=255)
                                         aTAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAgg                                                                                         <  1:309645/139‑1 (MQ=255)
                                                 gATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAgg                                                                                                                    <  1:46836/104‑1 (MQ=255)
                                                 gATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAgg                                                                                                                    >  2:46836/1‑104 (MQ=255)
                                                          tAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCa                                                                        >  2:284428/1‑139 (MQ=255)
                                                            gtgtAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAAt                                                                      >  1:863134/1‑139 (MQ=255)
                                                                 aGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGt                                                                 >  1:166836/1‑139 (MQ=255)
                                                                     aTTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       >  1:705255/1‑97 (MQ=255)
                                                                     aTTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       <  2:705255/97‑1 (MQ=255)
                                                                      ttACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTc                                                            >  2:846630/1‑139 (MQ=255)
                                                                       tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACaaaa                                                                                                                                     >  1:357811/1‑65 (MQ=255)
                                                                       tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACaaaa                                                                                                                                     <  2:357811/65‑1 (MQ=255)
                                                                       tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCg                                                           >  1:514886/1‑139 (MQ=255)
                                                                            tGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGc                                                      >  1:401121/1‑139 (MQ=255)
                                                                            tGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGc                                                      >  2:107077/1‑139 (MQ=255)
                                                                                   aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCgg                                                                                    >  1:1083924/1‑102 (MQ=255)
                                                                                   aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCgg                                                                                    <  2:1083924/102‑1 (MQ=255)
                                                                                   aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTg                                               >  2:333404/1‑139 (MQ=255)
                                                                                   aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTg                                               <  2:863134/139‑1 (MQ=255)
                                                                                        cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGcc                                                                                                          >  2:828018/1‑75 (MQ=255)
                                                                                        cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGcc                                                                                                          <  1:828018/75‑1 (MQ=255)
                                                                                        cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       >  2:568159/1‑78 (MQ=255)
                                                                                        cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       <  1:568159/78‑1 (MQ=255)
                                                                                        cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGct                                          <  2:166836/139‑1 (MQ=255)
                                                                                            acaTCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:983182/139‑1 (MQ=255)
                                                                                            acaTCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:846630/139‑1 (MQ=255)
                                                                                                  ttttACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGAt                                >  1:1164999/1‑139 (MQ=255)
                                                                                                        gtcgtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          <  2:941621/139‑1 (MQ=255)
                                                                                                           gtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCg                                            <  1:1053165/118‑1 (MQ=255)
                                                                                                           gtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCg                                            >  2:1053165/1‑118 (MQ=255)
                                                                                                            tACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCt                                                 >  1:911344/1‑112 (MQ=255)
                                                                                                            tACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCGAGAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCt                                                 <  2:911344/112‑1 (MQ=255)
                                                                                                             aCTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGc                     <  1:284428/139‑1 (MQ=255)
                                                                                                                 aCCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      >  2:102353/1‑118 (MQ=255)
                                                                                                                 aCCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:102353/118‑1 (MQ=255)
                                                                                                                   cTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          >  2:1086033/1‑128 (MQ=255)
                                                                                                                   cTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          <  1:1086033/128‑1 (MQ=255)
                                                                                                                      gcTTAATTCACGACAAGAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGTGCCGGTCAATGAAGGCAATGACGTGTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGTTTACTCTTTGGCCTGGATATc            <  2:1300007/138‑1 (MQ=255)
                                                                                                                       cTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCg           <  1:333404/139‑1 (MQ=255)
                                                                                                                                caacaaAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTg  >  2:706453/1‑139 (MQ=255)
                                                                                                                                caacaaAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTg  >  2:723508/1‑139 (MQ=255)
                                                                                                                                   |                                                                                                                                       
TCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTG  >  NC_000913/3088126‑3088392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A