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	120	56.0	1898522	99.4%	1887130	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,741,761	A→G	intergenic (+36/‑114)	yfiL → / → yfiR	DUF2799 domain‑containing lipoprotein YfiL/DUF4154 domain‑containing protein YfiR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,741,761	0	A	G	100.0%	115.9 / NA	33	intergenic (+36/‑114)	yfiL/yfiR	DUF2799 domain‑containing lipoprotein YfiL/DUF4154 domain‑containing protein YfiR
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/17); total (16/17)

CTTTCCTGCCAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTACTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGTTTTTCTCACCGA  >  NC_000913/2741626‑2741892

cTTTCCTGCCAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCa                                                                                                                                 <  1:569173/140‑1 (MQ=255)

  ttCCTGCCAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCAtt                                                                                                                               <  2:567431/140‑1 (MQ=255)

    ccTGCCAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATtgt                                                                                                                             >  1:101526/1‑140 (MQ=255)

         cAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGtttt                                                                                                                        <  1:772444/140‑1 (MQ=255)

            cTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTAtt                                                                                                                     >  2:786672/1‑140 (MQ=255)

                   aaTGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTcaca                                                                                                              <  1:786672/140‑1 (MQ=255)

                     tGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTcaca                                                                                                              <  1:426290/138‑1 (MQ=255)

                     tGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTcaca                                                                                                              >  2:426290/1‑138 (MQ=255)

                          aaaaTGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATtgatga                                                                                                       >  1:593920/1‑140 (MQ=255)

                                 cagccaACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTcaca                                                                                                              >  2:612789/1‑126 (MQ=255)

                                 cagccaACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTcaca                                                                                                              <  1:612789/126‑1 (MQ=255)

                                       aCTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGaaa                                                                                          <  2:657913/140‑1 (MQ=255)

                                          gCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGaaaaaa                                                                                       >  1:390018/1‑140 (MQ=255)

                                               aaGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGata                                                                                  <  1:589128/140‑1 (MQ=255)

                                                   aTGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACTATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATAtttt                                                                              <  2:361561/140‑1 (MQ=255)

                                                   aTGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATAtttt                                                                              >  2:283364/1‑140 (MQ=255)

                                                          aaaGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGc                                                                       >  2:113202/1‑140 (MQ=255)

                                                          aaaGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGc                                                                       >  1:279272/1‑140 (MQ=255)

                                                           aaGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCa                                                                      >  1:613815/1‑140 (MQ=255)

                                                                            gCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGa                                                     <  2:390018/140‑1 (MQ=255)

                                                                                gCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCa                                                 >  2:107702/1‑140 (MQ=255)

                                                                                      tACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGa                                           >  2:234038/1‑140 (MQ=255)

                                                                                           ttaaattaaTTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGaa                                      <  1:283364/140‑1 (MQ=255)

                                                                                           ttaaattaaTTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGaa                                      >  1:446918/1‑140 (MQ=255)

                                                                                            taaattaaTTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAg                                     <  2:279272/140‑1 (MQ=255)

                                                                                            taaattaaTTAAAACCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAg                                     <  1:234038/140‑1 (MQ=255)

                                                                                                         aCCCCACAAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATcc                        >  1:415975/1‑140 (MQ=255)

                                                                                                             cacaAATAAATTAAACATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGa                    <  1:113202/140‑1 (MQ=255)

                                                                                                                          aaCATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGTTTTtctc       <  2:407377/140‑1 (MQ=255)

                                                                                                                          aaCATAAGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGTTTTtctc       <  2:613815/140‑1 (MQ=255)

                                                                                                                               aaGATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGTTTTTCTCACCGa  >  1:74761/1‑140 (MQ=255)

                                                                                                                                 gATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGttt            <  1:35771/128‑1 (MQ=255)

                                                                                                                                 gATTTTGCTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGttt            >  2:35771/1‑128 (MQ=255)

CTTTCCTGCCAGCTGCAACAATGTTGAAAATGCCAGCCAACTGCATGAAGTATGGCAAAAAGGGGCTGATGAAAATGCCAGCACAATACGATTAAATTAATTAAAACCCCACAAATAAATTAAACATAAGATTTTACTCATTGTGTTTTATTTCTCACATTGATGACGGTCGCATGAAAAAATGATATTTTAATGAGCATTCTGAAAAAATATCGATGCATTTCGAGCGAAGATGGTGGGGATCCCTGAATGCGTTTTTCTCACCGA  >  NC_000913/2741626‑2741892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A