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
A1 F1 I1 R1 315 33.5 1889570 98.7% 1865005 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,513,581 C→T S180S (TCC→TCT)  nupC → nucleoside:H(+) symporter NupC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,513,5810CT100.0% 120.0 / NA 33S180S (TCC→TCT) nupCnucleoside:H(+) symporter NupC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/10);  total (23/10)

TAAAGATATCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCCATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGTTCAGCACC  >  NC_000913/2513503‑2513656
                                                                              |                                                                           
taAAGATATCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTAt                                                                           <  1:457733/81‑1 (MQ=255)
    gATATCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGtt                                                                       <  1:457734/81‑1 (MQ=255)
     atatCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTg                                                                      >  2:457778/1‑81 (MQ=255)
        tCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGt                                                                    <  1:457735/80‑1 (MQ=255)
         ccTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTg                                                                   >  2:457759/1‑80 (MQ=255)
            cGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATa                                                               >  2:457761/1‑81 (MQ=255)
             ggCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATa                                                               >  2:457763/1‑80 (MQ=255)
                aaaaTCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACAt                                                            >  2:457757/1‑80 (MQ=255)
                   aTCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGAcc                                                        <  1:457736/81‑1 (MQ=255)
                         cGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTg                                                  >  2:457779/1‑81 (MQ=255)
                            aaTCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGaa                                               >  2:457784/1‑81 (MQ=255)
                                gTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCg                                            >  1:457770/1‑80 (MQ=255)
                                gTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCg                                            >  1:457771/1‑80 (MQ=255)
                                  aTGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGaaa                                         >  1:457775/1‑81 (MQ=255)
                                        acCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATAcgtc                                   <  1:457737/81‑1 (MQ=255)
                                        acCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATAcgtc                                   >  1:457765/1‑81 (MQ=255)
                                        acCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATAcgtc                                   >  2:457783/1‑81 (MQ=255)
                                         ccATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGGAATAcgtcg                                  >  1:457781/1‑81 (MQ=255)
                                           aTGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGtt                                <  2:457738/81‑1 (MQ=255)
                                            tGGCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTtg                               <  2:457739/81‑1 (MQ=255)
                                              gCTGCCACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTtgct                             >  2:457769/1‑81 (MQ=255)
                                                  ccACGGCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTgcg                          <  2:457740/80‑1 (MQ=255)
                                                      ggCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTgg                      >  1:457790/1‑80 (MQ=255)
                                                       gCAATGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTAGAACCGAAATACGTCGTTGCTGCGCTGGTa                    >  2:457773/1‑81 (MQ=255)
                                                         aaTGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACt                  >  1:457786/1‑81 (MQ=255)
                                                          aTGTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACt                  >  2:457776/1‑80 (MQ=255)
                                                            gTCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGaa               >  2:457760/1‑81 (MQ=255)
                                                             tCCACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAAc              <  1:457741/81‑1 (MQ=255)
                                                               cACCGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACAt            >  1:457772/1‑81 (MQ=255)
                                                                  cGTGTCGATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGtt         >  1:457785/1‑81 (MQ=255)
                                                                        gATGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGTTCAGCAc   >  1:457774/1‑81 (MQ=255)
                                                                         aTGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGTTCAGCAcc  <  1:457742/81‑1 (MQ=255)
                                                                         aTGTCTATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGTTCAGCAcc  >  2:457788/1‑81 (MQ=255)
                                                                              |                                                                           
TAAAGATATCCTCGGCAAAATCTCCCGTAATCGTATGTACACCATGGCTGCCACGGCAATGTCCACCGTGTCGATGTCCATCGTTGGTGCATACATGACCATGCTGGAACCGAAATACGTCGTTGCTGCGCTGGTACTGAACATGTTCAGCACC  >  NC_000913/2513503‑2513656

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A