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
A4 F28 I1 R1	164	66.7	2276140	99.1%	2255654	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,455,873	G→A	intergenic (‑227/+454)	yfcV ← / ← sixA	putative fimbrial protein YfcV/phosphohistidine phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,455,873	0	G	A	100.0%	168.8 / NA	48	intergenic (‑227/+454)	yfcV/sixA	putative fimbrial protein YfcV/phosphohistidine phosphatase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/28); total (20/28)

CGGCATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCT  >  NC_000913/2455738‑2456007

cGGCATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGaaa                                                                                                                                    >  1:672659/1‑140 (MQ=255)

  gCATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGa                                                                                                                                  <  1:320513/140‑1 (MQ=255)

   cATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGAt                                                                                                                                 <  2:179448/140‑1 (MQ=255)

   cATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGAt                                                                                                                                 >  2:656111/1‑140 (MQ=255)

   cATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGAt                                                                                                                                 >  1:617297/1‑140 (MQ=255)

   cATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGAt                                                                                                                                 <  1:382656/140‑1 (MQ=255)

                       gTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTaaa                                                                                                             >  1:183952/1‑140 (MQ=255)

                             aaaaaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAaca                                                                                                       <  2:672659/140‑1 (MQ=255)

                             aaaaaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAaca                                                                                                       <  2:843991/140‑1 (MQ=255)

                              aaaaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAacac                                                                                                      <  1:386928/140‑1 (MQ=255)

                               aaaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACg                                                                                                     <  2:12462/140‑1 (MQ=255)

                                aaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGa                                                                                                    <  1:405976/140‑1 (MQ=255)

                                              tgtgGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAGAAAAACACGAAATATATATTTAGa                                                                                      <  2:482238/140‑1 (MQ=255)

                                                tgGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGaaa                                                                                    <  1:240251/140‑1 (MQ=255)

                                                tgGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTACCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGaaa                                                                                    <  1:656111/140‑1 (MQ=255)

                                                       gAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAgg                                                                             >  2:412133/1‑140 (MQ=255)

                                                        aaTAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGa                                                                            >  2:1127888/1‑140 (MQ=255)

                                                        aaTAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGa                                                                            <  1:852242/140‑1 (MQ=255)

                                                                  ttttCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATcaa                                                                  <  1:716399/140‑1 (MQ=255)

                                                                  ttttCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATcaa                                                                  <  2:353203/140‑1 (MQ=255)

                                                                       aCTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg                                                             <  2:530064/140‑1 (MQ=255)

                                                                           cccTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatgaatg                                                         >  1:732080/1‑140 (MQ=255)

                                                                             cTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGcc                                                       <  2:773874/140‑1 (MQ=255)

                                                                              tGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCa                                                      >  1:39698/1‑140 (MQ=255)

                                                                              tGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCa                                                      <  2:113538/140‑1 (MQ=255)

                                                                                     atttaatttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCtt                                               >  2:391103/1‑140 (MQ=255)

                                                                                     atttaatttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCtt                                               >  1:574313/1‑140 (MQ=255)

                                                                                     atttaatttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCtt                                               >  2:447161/1‑140 (MQ=255)

                                                                                         aatttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTaaaa                                           <  2:732080/140‑1 (MQ=255)

                                                                                            tttACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaac                                        <  2:617297/140‑1 (MQ=255)

                                                                                              tACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaa                                      <  2:992124/140‑1 (MQ=255)

                                                                                                 tAATGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAaacaaaca                                   <  2:574313/140‑1 (MQ=255)

                                                                                                  aaTGAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAacaaacaa                                  <  2:39698/140‑1 (MQ=255)

                                                                                                     gAGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGa                               <  1:412133/140‑1 (MQ=255)

                                                                                                      aGTAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGaa                              <  1:447161/140‑1 (MQ=255)

                                                                                                        tAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa                            >  1:231428/1‑140 (MQ=255)

                                                                                                        tAAATGTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa                            >  1:147141/1‑140 (MQ=255)

                                                                                                             gTAGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATaa                       >  2:415164/1‑140 (MQ=255)

                                                                                                               aGATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATg                     >  2:978379/1‑140 (MQ=255)

                                                                                                                gATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaaac                                    >  2:107453/1‑124 (MQ=255)

                                                                                                                gATTTAATTAATATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaaac                                    <  1:107453/124‑1 (MQ=255)

                                                                                                                   ttaattaaTATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                 <  1:1127888/140‑1 (MQ=255)

                                                                                                                     aattaatATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTg               >  1:784683/1‑140 (MQ=255)

                                                                                                                     aattaatATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTg               >  1:127080/1‑140 (MQ=255)

                                                                                                                      attaatATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTgg              <  1:978379/140‑1 (MQ=255)

                                                                                                                      attaatATATTGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTgg              >  2:857844/1‑140 (MQ=255)

                                                                                                                                tGATAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCg    >  2:857756/1‑140 (MQ=255)

                                                                                                                                  aTAGGAGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCt  <  2:1099061/140‑1 (MQ=255)

CGGCATGCGATCCAAAAAAACAGGTCGTAAAAAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCT  >  NC_000913/2455738‑2456007

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