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	696,470	C→T	100%	noncoding (35/75 nt)	glnX ←	tRNA‑Gln

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	696,470	0	C	T	100.0%	145.0 / ‑6.7	50	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (26/23); minor base G (0/1); total (26/24)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696330‑696607

cGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACGTCGGAATGCCGGAATTAg                                                                                                                                         >  1:728375/1‑143 (MQ=255)

  tCGCATCCGACATTGAAGGATAAGAAGTGAGAACAAGGCAGTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCGTGTTTAAGGTGGGTGGGATACGAGGAGTCGAACCTCGGAATGCCGGAATTAGaa                                                                                                                                       >  2:69372/1‑143 (MQ=255)

          gACATTGATGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCAGtcc                                                                                                                               >  2:676415/1‑141 (MQ=255)

           aCATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGcc                                                                                                                              >  1:230365/1‑143 (MQ=255)

               tGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGCATGCCGGCATTAGAATCCGGTGCCTTAc                                                                                                                          >  2:855400/1‑143 (MQ=255)

               tGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGGTTTAc                                                                                                                          >  2:653254/1‑143 (MQ=255)

                gAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAcc                                                                                                                         >  1:361794/1‑143 (MQ=255)

                 aaGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCg                                                                                                                        >  1:863920/1‑143 (MQ=255)

                    gATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCtt                                                                                                                     <  1:834170/143‑1 (MQ=255)

                       aaGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGc                                                                                                                  >  2:19696/1‑143 (MQ=255)

                        aGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCg                                                                                                                 <  1:314507/143‑1 (MQ=255)

                         gACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGGTCGTTGACCCGAGCTGTTTTAATGTGGCGGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGa                                                                                                                <  1:937572/143‑1 (MQ=25)

                          aCGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTCGCGAt                                                                                                               >  2:591952/1‑143 (MQ=255)

                            gtgtCAACATGGGATTCGACGTGGAAGGAACGCAGAACAGCAAAAAGGTGGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGGGCCTCGGAATGGCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATAc                                                                                                             <  2:200198/143‑1 (MQ=21)

                              gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCTGTGCCTTACCGCTTGGCGATAccc                                                                                                           >  1:356524/1‑143 (MQ=255)

                                  aCATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAAc                                                                                                       >  2:105295/1‑143 (MQ=255)

                                     tCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTgg                                                                                                    <  2:122231/143‑1 (MQ=255)

                                          ttCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCa                                                                                               <  2:321276/143‑1 (MQ=255)

                                               catgcaatgaaCGCACAACAGCAAAAAGCTCTCCGGAGCGAGCTTCTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTAc                                                                                          <  2:302859/138‑1 (MQ=21)

                                                aTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTACa                                                                                         >  1:458539/1‑143 (MQ=255)

                                                aTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACa                                                                                         >  1:617285/1‑143 (MQ=255)

                                                aTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCAATTACa                                                                                         >  1:617355/1‑143 (MQ=255)

                                                  tgaatggaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGATGATTCGAACCTCGGAATCCCGGAATTAGAATCCGGTGCCTTACCGTTTGGCGATACCCCAACTGGGTGCACTTACAAg                                                                                       <  2:94069/143‑1 (MQ=25)

                                                  tgaatgaaCGCAAAAAAGCGAAAAGCTCGCGGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAg                                                                                       <  2:605747/143‑1 (MQ=255)

                                                             aGAAAAGCAAAAAGCTCGCCGAAGCGGGCGTGCTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCAGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                            <  2:55085/143‑1 (MQ=21)

                                                                  aGCAAAAAGCTCGCCGAAGCGAGCTTTTTTACTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATa                                                                       >  1:646309/1‑143 (MQ=255)

                                                                  aGCAAAAAGCCCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATa                                                                       <  1:501329/143‑1 (MQ=255)

                                                                    cAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGCTTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACACGGTCCGCGCCTTGaacaca                                                                     >  2:324193/1‑139 (MQ=21)

                                                                      aaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCCCTTGCAAGGTAAGCGCCTTGAATAAAta                                                                   >  2:721123/1‑142 (MQ=255)

                                                                           cTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTg                                                              <  1:943508/143‑1 (MQ=255)

                                                                              gCCGATGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgggg                                                           <  2:85699/143‑1 (MQ=255)

                                                                               ccGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTGCAAGGTAAGCGTCTTGAATAAATTGGCTGGGGt                                                          >  1:205389/1‑143 (MQ=255)

                                                                                   aGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACCAGGTACGCATCTTGAATAAATTGGCTGGGGTACGa                                                      <  1:596100/143‑1 (MQ=255)

                                                                                                agtgtgGCTGGGGTACGAGCGTTCGCACCTCTGAATGCCGGAATTAGACTCCTGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTc                                         <  2:860003/141‑1 (MQ=25)

                                                                                                aaTGTGGCTGGCGTACGAGGATTCGAACCTCGGAACGCCGGAATTAGACTCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTc                                         <  1:807283/143‑1 (MQ=255)

                                                                                                      gCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCCACTGGGTGCACTTACAAGGTCAGCGTATTGAATACACTGGCTGGGGTACGAGGATTCGAACCTCTGAATg                                   >  1:93925/1‑143 (MQ=21)

                                                                                                        tGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGcc                                 <  1:312677/143‑1 (MQ=255)

                                                                                                         ggggTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGCTACGAGGATTCGAACCTCGGCATGCCg                                >  1:604241/1‑143 (MQ=255)

                                                                                                             tACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAAt                            <  1:325361/143‑1 (MQ=255)

                                                                                                                caaaaatCGAACCTCGGAATGCCGGAACTAGCAGCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAg                         <  1:119874/137‑1 (MQ=38)

                                                                                                                 aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCCGa                        >  1:465431/1‑143 (MQ=255)

                                                                                                                    aTTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGCGTGCACTTACAAGGTAAGCGCATTGAATAAATTGGCTGGGGTACGAGGCTTCGCACCGCGTGATGCCGGAACGAGaaac                     >  2:489203/1‑141 (MQ=21)

                                                                                                                     ttCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATcc                    <  1:920010/143‑1 (MQ=255)

                                                                                                                        gAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGt                 <  1:287244/143‑1 (MQ=255)

                                                                                                                         aaCCTGGGAATGCTGGAATTAGAATCCAGCGCCTTACCGCTTGGCGATACCCCAACTGGCTGCACTTACGCGGAAAGCGTCTTGAATAAAGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTg                <  2:513504/143‑1 (MQ=25)

                                                                                                                              cGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATGCGAACGGAGGAAGGCCGGAAACAGACACCgggagagca           >  2:51860/1‑136 (MQ=25)

                                                                                                                                      cGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACGACAACTGGGTGCACTTGCAAGGTAAGCGTCTTGAAGAAAATAGCCGTGGGACGTGGATTCGAACAACGGAACGCCGGAAACAGAATCCGGTACCAAACCgagggg   >  2:565162/1‑138 (MQ=255)

                                                                                                                                      cGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTACGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGTATCAGAATCCGGTGCCTTACCGCtcgt   >  2:477254/1‑140 (MQ=255)

                                                                                                                                      cGGAACGAGACTCCGTGGCCTTACCGCTTGGCGATACCCAAACTGGGTGAACTTACGAGGTTAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTgg   <  1:788005/143‑1 (MQ=21)

                                                                                                                                       ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGc  <  1:670342/143‑1 (MQ=255)

CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696330‑696607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A