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 F28 I1 R1 176 31.5 1082462 98.8% 1069472 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,779,579 T→C T1050A (ACC→GCC)  ypjA ← adhesin‑like autotransporter YpjA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,779,5790TC100.0% 93.8 / NA 28T1050A (ACC→GCC) ypjAadhesin‑like autotransporter YpjA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/15);  total (13/15)

CCGCTACCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGTACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGACCGCCCCTTCGAGT  >  NC_000913/2779443‑2779712
                                                                                                                                        |                                                                                                                                     
ccGCTACCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATGCCGTTAGTTGAGGCAGCCGCTGCTGGTTGCTGTGGCAAATAAACATCAACGTAGTGGAGTAGCAAAATTTTTACTCTATATTCGGAGGTGCCGGCAcc                                                                                                                                    >  2:227629/1‑140 (MQ=255)
ccGCTACCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCAcc                                                                                                                                    >  1:418543/1‑140 (MQ=255)
 cGCTACCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCt                                                                                                                                   >  1:537655/1‑140 (MQ=255)
     aCCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGcac                                                                                                                               <  1:356414/140‑1 (MQ=255)
      ccGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGcaca                                                                                                                              <  2:536002/140‑1 (MQ=255)
      ccGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGcaca                                                                                                                              <  1:427157/140‑1 (MQ=255)
              ttCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAattat                                                                                                                      >  2:206963/1‑140 (MQ=255)
               tCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAattatt                                                                                                                     <  1:479974/140‑1 (MQ=255)
                        gTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAg                                                                                                            >  1:56002/1‑140 (MQ=255)
                          cAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGcc                                                                                                          <  2:55342/140‑1 (MQ=255)
                             cGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGa                                                                                                       <  1:450860/140‑1 (MQ=255)
                                     aGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGccc                                                                                               <  1:206963/140‑1 (MQ=255)
                                          ccGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCt                                                                                          >  2:217063/1‑140 (MQ=255)
                                           cGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTg                                                                                         >  1:344731/1‑140 (MQ=255)
                                                 ttGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTgg                                                                                        >  1:369736/1‑135 (MQ=255)
                                                 ttGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTgg                                                                                        <  2:369736/135‑1 (MQ=255)
                                                           cgcTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCgg                                                                         >  1:103369/1‑140 (MQ=255)
                                                            gctgctGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGACGTCAGGTCGGc                                                                        <  2:367075/140‑1 (MQ=255)
                                                                        gCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATc                                                            >  1:41477/1‑140 (MQ=255)
                                                                                   aaCATCACCGTCGTTGAGTAGCAAACTGTTTGCTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTc                                                 >  1:119011/1‑140 (MQ=255)
                                                                                     cATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTccc                                               <  2:103369/140‑1 (MQ=255)
                                                                                     cATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTccc                                               <  1:254734/140‑1 (MQ=255)
                                                                                     cATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTccc                                               <  2:41477/140‑1 (MQ=255)
                                                                                                      aGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCt                              <  2:418543/140‑1 (MQ=255)
                                                                                                      aGCAAACTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCt                              <  2:56002/140‑1 (MQ=255)
                                                                                                            cTGTTTACTCTATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGt                        >  1:76/1‑140 (MQ=255)
                                                                                                                    tctATATTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGa                <  2:537655/140‑1 (MQ=255)
                                                                                                                         atTCGCAGTTGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGACCGcc           <  1:486355/140‑1 (MQ=255)
                                                                                                                                  tGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGACCGCCCCTTCGAGt  >  2:340349/1‑140 (MQ=255)
                                                                                                                                  tGCTGGCACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGACCGCCCCTTCGAGt  >  1:73828/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                     
CCGCTACCGGAAAGTTCATTGGTTGTCAGCGTATTGTAGATACCGTTAGTTGTGGCAGGCGCTGCTGTTTGTGCTGACAAATAAACATCACCGTCGTTGAGTAGCAAACTGTTTACTCTATATTCGCAGTTGCTGGTACCTGCACAGGAATTATTGCTGTTAAGCCAGACACTGCCCCGGCTGGCAGCCGTCAGGTCGGCAAGCGTGGTATCGACGCCATTTCCCAGAGTCAATGTCGCGCTATCGGTAATCCGGACCGCCCCTTCGAGT  >  NC_000913/2779443‑2779712

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A