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
A13 F87 I0 R1 87 48.8 1893308 89.3% 1690724 142.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,307,298 G→A 14.2% P168S (CCC→TCC)  alsK ← D‑allose kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,307,2980GA14.2% 69.3 / 4.6 35P168S (CCC→TCC) alsKD‑allose kinase
Reads supporting (aligned to +/- strand):  ref base G (16/13);  new base A (2/3);  total (18/17)
Fisher's exact test for biased strand distribution p-value = 6.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.74e-01

TTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTCTACTA  >  NC_000913/4307157‑4307429
                                                                                                                                             |                                                                                                                                   
ttgccGCATGGACGAAACGCTCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGCATTAGCGCCATGCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAggggg                                                                                                                                    <  2:763791/140‑1 (MQ=255)
     gCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGCCATCTCTCCGAGGGGGATATg                                                                                                                               >  1:647499/1‑143 (MQ=255)
     gCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGAACATATCTCCCAggggggcatg                                                                                                                               >  2:639911/1‑138 (MQ=255)
      cATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCCCCCTGGGAGATATGa                                                                                                                              <  1:85535/143‑1 (MQ=255)
       aTGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCCCTCTGGGAGATATGAc                                                                                                                             <  1:943512/143‑1 (MQ=255)
        tGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGAcc                                                                                                                            >  1:669170/1‑143 (MQ=255)
                  gcgcgccCAATGGGTCTTTTCGGGGCTGTCGCTCGTACCAGCGTCTTAGCGCCCTTCCAGAGCAATTGGTTTCGAGGCACCCAGGATAGCCACACGCGCAGTTTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCt                                                                                                                  <  2:248153/140‑1 (MQ=255)
                       cgcAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCAAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTTCTATGTCCCAGGTGGATATGACCCACTTCGCGTGCcac                                                                                                             >  2:600611/1‑143 (MQ=255)
                                 caTTGCGCGGCTGTTGTTCGTACGAGTGTCTTAGCGCCATTTCAGGGCAATTGGTTGCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGGCATATCTCCCAGGGGGGTATGACCCAGTTCGCCTGCCACACCGTGTGCa                                                                                                   <  2:262222/142‑1 (MQ=255)
                                    ttCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCGGGGGGATATGACCCAGTTGGCCTGCCACACCGCGTCCGccc                                                                                                >  1:29216/1‑143 (MQ=255)
                                                               ttAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACt                                                                     <  1:135047/143‑1 (MQ=255)
                                                                tAGCGCCATCCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTGGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTg                                                                    <  2:434873/143‑1 (MQ=255)
                                                                  ccgcCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCg                                                                  <  1:566000/142‑1 (MQ=255)
                                                                             gatcAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATccc                                                       <  1:142369/140‑1 (MQ=255)
                                                                                gagttGGTTTCCAGGCACCCAGGAGTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGt                                                    <  2:820602/140‑1 (MQ=255)
                                                                                 agtgtgTTGCCTGGCTCTCAGCATTGCCTCACGCGCAGTGTTGGGTCATATCTCCCTGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTa                                                   <  1:386745/138‑1 (MQ=255)
                                                                                    tGGTTTCCAGGCCCCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCg                                                <  1:549087/143‑1 (MQ=255)
                                                                                      gTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCGGCCACACCGTGTGCGCCCGTCCACGGCGCGCCGTTCATCTCCACTGCGACCCCCGTCGCCGtcgcgtg                                              >  1:126820/1‑137 (MQ=255)
                                                                                            aGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACGGCGAACCCCATCCCCGTACCGAGATAGgc                                        >  1:345321/1‑143 (MQ=255)
                                                                                            aGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATAGGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCAGCCACACTGCGAACCCCGTACCCGTCACGAGATAGgc                                        >  1:827188/1‑143 (MQ=255)
                                                                                             ggCCCCCAGGAGTGCCACACGCGCAGTGTTGGGTCATAGCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGGCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGgcc                                       <  1:217380/143‑1 (MQ=255)
                                                                                             ggCACCCAGGATTGCCACACGCGCAGTGTTGGGACATATCTCCCAGGGGGATATGACCCAGTTCGCCCACCGCCCCGTGTGCACCCGGCCACGGCGCACCGCTCATCCACCGTGCGAACCCCATCCCCCTACCGCGACCGgcc                                       >  2:765262/1‑143 (MQ=255)
                                                                                              gCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTACACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGGACCGGGATAGgccg                                      >  1:850634/1‑143 (MQ=255)
                                                                                                  ccAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAg                                  >  1:918923/1‑143 (MQ=255)
                                                                                                   cAGGATTGCCACACGCGCAGGGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATc                                                                           >  1:388236/1‑101 (MQ=255)
                                                                                                   cAGGATTGCCACACGCGCAGGGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATc                                                                           <  2:388236/101‑1 (MQ=255)
                                                                                                    aGGATTGCCACAGGCGCAGTTTTGGGTCATACCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTTTGCACCCGTCCACGCCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGaa                                <  2:482306/143‑1 (MQ=255)
                                                                                                     ggATTGCCACACGCGCAGTGTTGAGTCATCTCTCACACACACATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAAc                               <  1:390799/143‑1 (MQ=255)
                                                                                                               tcgtgcAGTGTTGTGTCATATCTCCCAGTGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCTCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGc                     <  1:88703/139‑1 (MQ=255)
                                                                                                               acGCGCAGTGTTGGGTCATATCTCCCAGGGGGCTATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACCCTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGGTGTTGc                     >  1:645939/1‑143 (MQ=255)
                                                                                                                       tgtTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCGCCCGTCCACGGCGCACCGTTCATCCACACTGCGCACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGcc             >  1:415405/1‑142 (MQ=255)
                                                                                                                         ttGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGt           >  1:762727/1‑143 (MQ=255)
                                                                                                                         ttGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTAGTTGCGTAAGGCGGt           >  1:245071/1‑143 (MQ=255)
                                                                                                                            ggTCATATCCCCCTGGGAGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCCGAACCAGTTGTTGCGTAAGGCGGttta        >  1:778742/1‑142 (MQ=255)
                                                                                                                             gTCTTATCGCCCGGTGTGAGATGCCCCCGTCCGCCGCCCACACCGTGTGCACCCGACCCCGGCGCCACGGTGATCTACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTc       <  2:173793/143‑1 (MQ=255)
                                                                                                                              tCATATCCCCCTGGGAGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTct      >  1:533628/1‑143 (MQ=255)
                                                                                                                                  atCTCCCAGGGGGATATGACCCAGTTCTCCTGCCACACCCTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTCCGAACCCCATCCCCGTACCGAGATAGGCCCCCAGAACACGTTATTGCGAAAGGCGGTTTTatccta  >  2:368879/1‑143 (MQ=255)
                                                                                                                                             |                                                                                                                                   
TTTCCGCATGGACGAAAAGATCGCGCAATGGGTAATTTCGGGGCTGTTGTTCGTACCAGCGTCTTAGCGCCATTCCAGAGCAATTGGTTTCCAGGCACCCAGGATTGCCACACGCGCAGTGTTGGGTCATATCTCCCAGGGGGATATGACCCAGTTCGCCTGCCACACCGTGTGCACCCGTCCACGGCGCACCGTTCATCCACACTGCGAACCCCATCCCCGTACCGAGATAGGCCGCCAGAACCAGTTGTTGCGTAAGGCGGTTTTCTACTA  >  NC_000913/4307157‑4307429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A