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
A9 F28 I1 R1 138 91.1 3071990 99.2% 3047414 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,521,444 A→G L193L (TTG→CTG)  yjhF ← KpLE2 phage‑like element; putative transporter YjhF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,521,4440AG100.0% 141.3 / NA 41L193L (TTG→CTG) yjhFKpLE2 phage‑like element; putative transporter YjhF
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (11/30);  total (11/30)

ACCGGCAGCATTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAATACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCAAAAAACCGTGTGCGACCAG  >  NC_000913/4521305‑4521579
                                                                                                                                            |                                                                                                                                       
aCCGGCAGCATTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGGCGCGCCGGGAGAGGGTATA‑TTTCCCCCTTTTTTTAAAGCGTCCGGGATAAAGCGCTGGGAGAAATTTTTTaa                                                                                                                                         >  2:702021/1‑140 (MQ=255)
       gcaTTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCggg                                                                                                                                  <  1:12671/140‑1 (MQ=255)
       gcaTTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCggg                                                                                                                                  <  2:1414512/140‑1 (MQ=255)
        caTTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGCGGCGCCGGGAGGGGGTATA‑TTTCCCTCTTTTTTTAAGGGCGCCGGAACAATGAGCTGGTAGAGTTTTTTAAGTACCGGGc                                                                                                                                 >  2:202647/1‑140 (MQ=255)
            gCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCa                                                                                                                             <  1:705978/140‑1 (MQ=255)
            gCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCa                                                                                                                             <  1:433262/140‑1 (MQ=255)
            gCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCa                                                                                                                             <  1:285714/140‑1 (MQ=255)
            gCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGGCGCCCCGAGAGAGGCGATA‑TTCCCCCCCTTTTTTAAGGCGTCCCGGATAATGCGCTGGCAGAATTTATTCCGTACCGGGgcgcc                                                                                                                             >  2:1286716/1‑139 (MQ=255)
                  agaAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAAt                                                                                                                       <  2:69336/140‑1 (MQ=255)
                  agaAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCCAGAGAGGCTATA‑TTTCACCCTTTTTTTAAAGCGTCCGGGATAAAGCGCTGGCAGAATTTATTTAGTACCCGGCCGCCAAGaaa                                                                                                                       >  2:945725/1‑139 (MQ=255)
                     aaaCTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATaaa                                                                                                                    <  2:1142742/140‑1 (MQ=255)
                          gATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGGCGCGCCGAGAGAGGGTATA‑TTTCCCTCTTTTTTTAAAGCGGCCGGGATAATGCGCTGGGAGAATTTATTTAGTACCCGGCCGCAAAGAATaaaaggtg                                                                                                               >  2:929051/1‑135 (MQ=255)
                            tCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGa                                                                                                             <  2:746456/140‑1 (MQ=255)
                            tCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGGCGCGCCCAGAGAGGCCATATTTCCCCCCTTTTTTAAA‑GCGGCCCGAATAAAGCGCTGGCAGAAATTATTTAGTACCCGGCCGCCAAGAAAAAAAGGTggg                                                                                                             >  2:332055/1‑139 (MQ=255)
                               cAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATg                                                                                                          <  1:202647/140‑1 (MQ=255)
                               cAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATg                                                                                                          <  1:1286716/140‑1 (MQ=255)
                               cAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATg                                                                                                          <  2:287372/140‑1 (MQ=255)
                               cAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATg                                                                                                          <  1:702021/140‑1 (MQ=255)
                                 aaGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGcc                                                                                                        <  2:4237/140‑1 (MQ=255)
                                   gCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGa                                                                                                      <  1:173260/140‑1 (MQ=255)
                                    ccTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGAc                                                                                                     <  1:401427/140‑1 (MQ=255)
                                       ggCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGGTATA‑TTTCCCTCTTTTTTTAAAGCGTCCGGGATAATGCGCTGGCAGAATTTATTTAGTACCGGGCCGCAAAGAATAAAGAGTGGGATGCCGACaaa                                                                                                  >  2:1373265/1‑139 (MQ=255)
                                       ggCATTTCGCTTTCGCTGAATCGGCGGGGCGCGCCCAGAGAGGCTATA‑TTTCCCTCTTTTTTTAAAGCGGCCCGGATAATGCGCTGGCAGAAATTTTTTAGTACCGGGCCGCCAAAAAAAAAAGTTGGGATGCCCACaaa                                                                                                  >  2:291101/1‑139 (MQ=255)
                                         cATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGa                                                                                                <  1:945725/140‑1 (MQ=255)
                                         cATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGa                                                                                                <  2:740410/140‑1 (MQ=255)
                                           tttcgctttcgcTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATa                                                                                              <  1:929051/140‑1 (MQ=255)
                                             tcgctttcgctGAATCGGCGGGGCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTTAAAGCGTCCGGGAAAAAGCGCCGGCAGAATTTATTTAGTACCGGGCCGCCAAGAAAAAAAGGTGGGATGCCGACAATGATAcc                                                                                            >  2:864722/1‑140 (MQ=255)
                                              cgctttcgctGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCg                                                                                           <  2:832353/140‑1 (MQ=255)
                                              cgctttcgctGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCg                                                                                           <  1:332055/140‑1 (MQ=255)
                                                         aaTCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTAc                                                                                <  1:1373265/140‑1 (MQ=255)
                                                          aTCGTCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTAcc                                                                               <  2:1411321/140‑1 (MQ=255)
                                                          aTCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTAcc                                                                               <  1:864722/140‑1 (MQ=255)
                                                          aTCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTAcc                                                                               <  1:744128/140‑1 (MQ=255)
                                                             ggcggGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTAcggat                                                                            <  1:1099461/140‑5 (MQ=255)
                                                                        ccGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAgc                                                                 <  2:1013274/140‑1 (MQ=255)
                                                                            gagagGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCa                                                             >  1:927131/1‑140 (MQ=255)
                                                                                           cccTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCata                                                           >  1:914861/1‑128 (MQ=255)
                                                                                           cccTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCata                                                           <  2:914861/128‑1 (MQ=255)
                                                                                           cccTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGAt                                               >  1:866062/1‑140 (MQ=255)
                                                                                            ccTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATa                                              >  2:1193416/1‑140 (MQ=255)
                                                                                                ttttttAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAg                                          >  1:691733/1‑140 (MQ=255)
                                                                                                          gCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCggg                                >  1:1389914/1‑140 (MQ=255)
                                                                                                          gCGTCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCATGGCGATAACAGTCGGGCCggg                                >  2:242145/1‑140 (MQ=255)
                                                                                                             tCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTg                             >  2:469436/1‑140 (MQ=255)
                                                                                                             tCCGGAATAATGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTg                             >  1:1031138/1‑140 (MQ=255)
                                                                                                                      atGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCaa                    >  1:431277/1‑140 (MQ=255)
                                                                                                                       tGCGCTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCaaa                   >  2:390831/1‑140 (MQ=255)
                                                                                                                           cTGGCAGAATTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCAAAAAAc               <  1:60301/140‑1 (MQ=255)
                                                                                                                                   aTTTATTCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCAAAAAACCGTGTGCg       <  2:1389914/140‑1 (MQ=255)
                                                                                                                                        ttCAGTACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCAAAAAACCGTGTGCGACCAg  <  1:291101/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                       
ACCGGCAGCATTGCCGTGAGAAAACTGATCCCAAAGCCTGGCATTTCGCTTTCGCTGAATCGGCGGGTCGCGCCGAGAGAGGCTATA‑TTCCCCTCTTTTTTAAAGGCGTCCGGAATAATGCGCTGGCAGAATTTATTCAATACCGGGCCGCAAAGAATAAAGGTTGGAATGCCGACAATGATACCGTATATCAGTACCAATCCTACATCAGCGCCATATTCCCTGGCGATAACAGTCGGGCCGGGGTGCGGCGGCAAAAAACCGTGTGCGACCAG  >  NC_000913/4521305‑4521579

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A