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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,588	G→A	pseudogene (162/2439 nt)	yqiG →	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,588	0	G	A	100.0%	150.7 / NA	47	pseudogene (162/2439 nt)	yqiG	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/27); total (20/27)

GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAC  >  NC_000913/3187460‑3187708

gTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                <  2:1233629/139‑1 (MQ=255)

 ttGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCt                                                                                                               >  1:1036089/1‑139 (MQ=255)

  tGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              >  1:322255/1‑139 (MQ=255)

  tGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              >  2:477175/1‑139 (MQ=255)

  tGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              >  1:1139871/1‑139 (MQ=255)

        caacaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTc                                                                                                        <  1:477175/139‑1 (MQ=255)

          acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                      <  2:588846/139‑1 (MQ=255)

          acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                      <  1:280432/139‑1 (MQ=255)

           caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                     <  1:953475/139‑1 (MQ=255)

             aaGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATg                                                                                                   <  2:1209471/139‑1 (MQ=255)

                    aaTCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              >  2:1486800/1‑121 (MQ=255)

                    aaTCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              <  1:1486800/121‑1 (MQ=255)

                          aGCCGAAGATCGTGAAAACGTTTACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                           >  2:243765/1‑118 (MQ=255)

                          aGCCGAAGATCGTGAAAACGTTTACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                           <  1:243765/118‑1 (MQ=255)

                          aGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGAt                                                                                      >  1:1304953/1‑139 (MQ=255)

                                      tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAGTCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTg                                                                            <  2:1212019/137‑1 (MQ=255)

                                      tGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTg                                                                            >  1:1212019/1‑137 (MQ=255)

                                              ttAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                  <  2:1036089/139‑1 (MQ=255)

                                                   cTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGacac                                                             <  2:515122/139‑1 (MQ=255)

                                                     ttCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                           <  2:322255/139‑1 (MQ=255)

                                                      tCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                           >  1:985980/1‑90 (MQ=255)

                                                      tCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                           <  2:985980/90‑1 (MQ=255)

                                                       cccAATTTGAAACTGATGGCCAAGTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                         <  2:1304953/139‑1 (MQ=255)

                                                            tttGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATaa                                                                                    >  1:254269/1‑107 (MQ=255)

                                                            tttGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATaa                                                                                    <  2:254269/107‑1 (MQ=255)

                                                               gAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTaa                                                 <  1:1707660/139‑1 (MQ=255)

                                                                    tGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACatta                                            <  1:788939/139‑1 (MQ=255)

                                                                      aTGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattatt                                          <  2:1139871/139‑1 (MQ=255)

                                                                      aTGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattatt                                          >  2:734023/1‑139 (MQ=255)

                                                                        ggCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAg                                        >  1:188870/1‑139 (MQ=255)

                                                                                                    tAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc            <  2:188870/139‑1 (MQ=255)

                                                                                                       gCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              <  2:1350800/38‑1 (MQ=255)

                                                                                                       gCACTCTGATTAATAATAAGAGGACACCAATCCACCtt                                                                                                              >  1:1350800/1‑38 (MQ=255)

                                                                                                        cACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                       >  2:1621477/1‑76 (MQ=255)

                                                                                                        cACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                       <  1:1621477/76‑1 (MQ=255)

                                                                                                          ctctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCa      <  1:734023/139‑1 (MQ=255)

                                                                                                              gATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc            <  2:1164076/129‑1 (MQ=255)

                                                                                                              gATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAc  >  2:654828/1‑139 (MQ=255)

                                                                                                              gATTAATAAGAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAc            >  1:1164076/1‑129 (MQ=255)

                                                                                                               aTTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                  >  2:1259892/1‑74 (MQ=255)

                                                                                                               aTTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                  <  1:1259892/74‑1 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                           <  2:1730955/71‑1 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                           >  1:1730955/1‑71 (MQ=255)

                                                                                                                             gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                >  2:1527780/1‑62 (MQ=255)

                                                                                                                             gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                <  1:1411483/62‑1 (MQ=255)

                                                                                                                             gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                >  2:1411483/1‑62 (MQ=255)

                                                                                                                             gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGa                                                                <  1:1527780/62‑1 (MQ=255)

GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAAC  >  NC_000913/3187460‑3187708

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A