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
A5 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,790,538 A→G S270P (TCT→CCT)  tdh ← L‑threonine 3‑dehydrogenase, NAD(P)‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,790,5380AG96.1% 174.6 / ‑1.9 51S270P (TCT→CCT) tdhL‑threonine 3‑dehydrogenase, NAD(P)‑binding
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (27/22);  total (28/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.60e-01

TGGGTAATGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGACATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCGGTCATGCCTAACT  >  NC_000913/3790405‑3790669
                                                                                                                                     |                                                                                                                                   
tGGGTAATGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCatat                                                                                                                                >  1:293036/1‑139 (MQ=255)
      aTGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGAcg                                                                                                                          <  2:1028488/139‑1 (MQ=255)
      aTGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGACATATCAGAcg                                                                                                                          <  1:229647/139‑1 (MQ=255)
      aTGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGACATATCAGAcg                                                                                                                          >  2:229647/1‑139 (MQ=255)
           tcgCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGa                                                                                                                     <  2:734339/137‑1 (MQ=255)
            ggCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGaa                                                                                                                    >  1:1016545/1‑139 (MQ=255)
            ggCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGaa                                                                                                                    >  2:475242/1‑139 (MQ=255)
                                       aGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGt                                                                                         <  2:958378/139‑1 (MQ=255)
                                           ccgccATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGAtt                                                                                     >  2:481510/1‑139 (MQ=255)
                                             gccATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCa                                                                                   <  1:906461/139‑1 (MQ=255)
                                                        ccAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCTTATCAGACGGCGGAATACCGAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGc                                                                        >  1:265211/1‑139 (MQ=255)
                                                        ccAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGa                                                                                                                            >  2:973242/1‑87 (MQ=255)
                                                        ccAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGa                                                                                                                            <  1:973242/87‑1 (MQ=255)
                                                            gTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATgg                                                                    >  1:618858/1‑139 (MQ=255)
                                                            gTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATgg                                                                    >  2:863670/1‑139 (MQ=255)
                                                             tttCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGt                                                                   >  2:28356/1‑139 (MQ=255)
                                                                    cATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAAc                                                            <  1:475242/139‑1 (MQ=255)
                                                                       ctcACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCt                                                         >  1:622435/1‑139 (MQ=255)
                                                                       ctcACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCt                                                         >  2:728363/1‑139 (MQ=255)
                                                                           cGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTggcg                                                     <  2:618858/139‑1 (MQ=255)
                                                                            gACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTggcgg                                                    <  2:622435/139‑1 (MQ=255)
                                                                                 tAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCacac                                               >  1:268992/1‑139 (MQ=255)
                                                                                 tAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCAc                                               >  1:1023113/1‑139 (MQ=255)
                                                                                 tAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCAc                                               >  1:617341/1‑139 (MQ=255)
                                                                                     tACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGa                                           <  1:863670/139‑1 (MQ=255)
                                                                                     tACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGa                                           <  2:265211/139‑1 (MQ=255)
                                                                                          ttAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACAttt                                      >  2:449748/1‑139 (MQ=255)
                                                                                            aaTGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGTAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGAc                                          <  1:792948/133‑1 (MQ=255)
                                                                                            aaTGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGAc                                          >  2:792948/1‑133 (MQ=255)
                                                                                             aTGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCGATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCa                                   >  1:1073769/1‑139 (MQ=255)
                                                                                                 aCAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGAcc                               <  1:479646/139‑1 (MQ=255)
                                                                                                  cAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGgc                                                                                               >  1:84936/1‑74 (MQ=255)
                                                                                                  cAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGgc                                                                                               <  2:84936/74‑1 (MQ=255)
                                                                                                  cAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCTCCGTGATTCTTGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGAc                                          <  1:685158/127‑1 (MQ=255)
                                                                                                  cAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGAc                                          >  2:685158/1‑127 (MQ=255)
                                                                                                  cAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCg                              >  1:447626/1‑139 (MQ=255)
                                                                                                       cTTTAAAGATCACTTTGGTCCAGTCGATATGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCTTGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATc                         >  1:538650/1‑139 (MQ=255)
                                                                                                          tAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTggcg                                                     >  1:467993/1‑108 (MQ=255)
                                                                                                          tAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTggcg                                                     <  2:467993/108‑1 (MQ=255)
                                                                                                          tAAAGATCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCaaa                      >  2:372592/1‑139 (MQ=255)
                                                                                                                tCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGgtgt                                                                             >  2:260846/1‑78 (MQ=255)
                                                                                                                tCACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGgtgt                                                                             <  1:260846/78‑1 (MQ=255)
                                                                                                                 cACTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGc                                                                        <  2:717695/82‑1 (MQ=255)
                                                                                                                 cACTTTGGTCCAGTCGATAGGCATATCAAACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGc                                                                        >  1:717695/1‑82 (MQ=255)
                                                                                                                  aCTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCgg              <  1:28356/139‑1 (MQ=255)
                                                                                                                  aCTTTGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCgg              <  1:481510/139‑1 (MQ=255)
                                                                                                                    tttGGTCCAGTCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCGGTc            <  1:728363/139‑1 (MQ=255)
                                                                                                                              tCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGa                                           <  2:512961/98‑1 (MQ=255)
                                                                                                                              tCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGa                                           >  1:512961/1‑98 (MQ=255)
                                                                                                                              tCGATAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCGGTCATGCCTAACt  >  2:1091549/1‑139 (MQ=255)
                                                                                                                                  tAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGccgccg                                                                                          <  1:1074983/47‑1 (MQ=255)
                                                                                                                                  tAGGCATATCAGACGGCGGAATACCCAGCATCGCAATACGGccgccg                                                                                          >  2:1074983/1‑47 (MQ=255)
                                                                                                                                     |                                                                                                                                   
TGGGTAATGATCGGCGAAAGATCGAGGCCAGACTGAATCAGCGCCGCCATCTTGTACCAGGTTTCAAACATCTCACGACCGTAAATACCTTTAATGAACAAGCCTTTAAAGATCACTTTGGTCCAGTCGATAGACATATCAGACGGCGGAATACCCAGCATCGCAATACGGCCGCCGTGATTCATGGTGTCAAGCATGGTACGAAACGCTGGCGGCGCACCGGACATTTCCAGACCGACATCAAAACCTTCGGTCATGCCTAACT  >  NC_000913/3790405‑3790669

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A