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 4,319,653 G→A F337F (TTC→TTT)  phnI ← carbon‑phosphorus lyase core complex subunit PhnI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,319,6530GA100.0% 197.6 / NA 54F337F (TTC→TTT) phnIcarbon‑phosphorus lyase core complex subunit PhnI
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (21/33);  total (21/33)

TAGGCAAAGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGGAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACGAA  >  NC_000913/4319575‑4319730
                                                                              |                                                                             
tAGGCAAAGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGaaa                                                                             <  1:862597/81‑1 (MQ=255)
   gCAAAGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATc                                                                          <  1:862598/81‑1 (MQ=255)
    cAAAGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATc                                                                          >  1:862672/1‑80 (MQ=255)
       aGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACg                                                                      >  2:862657/1‑81 (MQ=255)
            tAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTg                                                                 <  2:862599/81‑1 (MQ=255)
              gCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTgg                                                                <  1:862600/80‑1 (MQ=255)
                cGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTggggg                                                             <  2:862601/81‑1 (MQ=255)
                 gCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTgggg                                                              >  2:862674/1‑79 (MQ=255)
                 gCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGa                                                            <  2:862602/81‑1 (MQ=255)
                     aGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGttt                                                        <  2:862605/81‑1 (MQ=255)
                     aGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGttt                                                        <  2:862604/81‑1 (MQ=255)
                     aGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGtt                                                         <  1:862603/80‑1 (MQ=255)
                      gATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGttt                                                        >  1:862652/1‑80 (MQ=255)
                      gATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTg                                                       <  2:862606/81‑1 (MQ=255)
                       aTTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGttt                                                        >  1:862700/1‑79 (MQ=255)
                        ttAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAg                                                     >  1:862685/1‑81 (MQ=255)
                          aGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgt                                                   >  2:862675/1‑81 (MQ=255)
                          aGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgt                                                   >  2:862665/1‑81 (MQ=255)
                           gCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgtg                                                  >  2:862682/1‑81 (MQ=255)
                           gCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgtg                                                  >  2:862651/1‑81 (MQ=255)
                           gCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgtg                                                  <  1:862608/81‑1 (MQ=255)
                           gCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgt                                                   <  1:862607/80‑1 (MQ=255)
                           gCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgt                                                   <  1:862609/80‑1 (MQ=255)
                             cATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGgtgt                                                 >  1:862668/1‑80 (MQ=255)
                               tGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTgag                                              <  1:862610/81‑1 (MQ=255)
                               tGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTgag                                              <  1:862611/81‑1 (MQ=255)
                                     tGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAg                                        >  2:862677/1‑81 (MQ=255)
                                       cTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGcc                                      <  2:862612/81‑1 (MQ=255)
                                       cTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGc                                       <  2:862613/80‑1 (MQ=255)
                                          cTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCt                                     <  1:862614/79‑1 (MQ=255)
                                          cTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTg                                    <  2:862616/80‑1 (MQ=255)
                                          cTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGc                                   <  1:862617/81‑1 (MQ=255)
                                          cTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGc                                   <  1:862615/81‑1 (MQ=255)
                                            gTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCgg                                 >  1:862664/1‑81 (MQ=255)
                                             ttGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCgg                                 <  1:862619/80‑1 (MQ=255)
                                             ttGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCg                                  <  2:862618/79‑1 (MQ=255)
                                             ttGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGc                                >  2:862666/1‑81 (MQ=255)
                                              tGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCt                               >  2:862684/1‑81 (MQ=255)
                                               gCAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCt                               <  1:862620/80‑1 (MQ=255)
                                                cAGACGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTc                             <  1:862621/81‑1 (MQ=255)
                                                   aCGTTTGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGAc                          <  2:862622/81‑1 (MQ=255)
                                                      tttGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGtt                       <  1:862623/81‑1 (MQ=255)
                                                      tttGAGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGtt                       <  2:862624/81‑1 (MQ=255)
                                                          aGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTc                    <  1:862626/80‑1 (MQ=255)
                                                          aGTAGCTCCAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCg                   <  1:862625/81‑1 (MQ=255)
                                                                  cAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCAtgt             <  1:862627/79‑1 (MQ=255)
                                                                  cAGTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGc           >  2:862687/1‑81 (MQ=255)
                                                                    gTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGc           >  1:862683/1‑79 (MQ=255)
                                                                    gTTCGGCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGc           >  1:862680/1‑79 (MQ=255)
                                                                        ggCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCAc     >  1:862694/1‑81 (MQ=255)
                                                                        ggCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCAc     >  1:862663/1‑81 (MQ=255)
                                                                         gCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACg    <  2:862630/81‑1 (MQ=255)
                                                                         gCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACg    <  2:862629/81‑1 (MQ=255)
                                                                         gCCTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACg    <  1:862628/81‑1 (MQ=255)
                                                                           cTGAAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACGaa  >  1:862673/1‑81 (MQ=255)
                                                                              |                                                                             
TAGGCAAAGTTGTAGCCGCTCAGATTAGCCATGGTTCTGCTCCTGTTGCAGACGTTTGAGTAGCTCCAGTTCGGCCTGGAAATCGACGTAGTGGGGGAGTTTGAGGTGTGAGACAAAGCCTGCGGCTTCGACGTTGTCGGCATGTGCCAGCACGAA  >  NC_000913/4319575‑4319730

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