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
A19 F60 I1 R1	18	74.2	2511834	99.1%	2489227	137.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,455,892	T→A	intergenic (‑246/+435)	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	2,455,892	0	T	A	96.5%	193.4 / ‑0.9	57	intergenic (‑246/+435)	yfcV/sixA	putative fimbrial protein YfcV/phosphohistidine phosphatase
Reads supporting (aligned to +/- strand): ref base T (1/1); new base A (25/30); total (26/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAA  >  NC_000913/2455769‑2456028

aaaTGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACg                                                                                                                          <  1:1102081/140‑1 (MQ=255)

          gTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAatatatat                                                                                                                <  1:323494/140‑1 (MQ=255)

               tgtgGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGa                                                                                                           >  1:514665/1‑140 (MQ=255)

                   gggTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGaaaaa                                                                                                       <  2:493519/140‑1 (MQ=255)

                         aaTAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGa                                                                                                 <  2:642782/140‑1 (MQ=255)

                              tGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCat                                                                                            >  2:510807/1‑140 (MQ=255)

                              tGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCat                                                                                            <  2:844400/140‑1 (MQ=255)

                              tGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCat                                                                                            <  1:424160/140‑1 (MQ=255)

                                aTGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGCGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCatat                                                                                          >  2:622111/1‑140 (MQ=255)

                                   ttttCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATcaa                                                                                       >  1:1113696/1‑140 (MQ=255)

                                        aCTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg                                                                                  <  2:506259/140‑1 (MQ=255)

                                         cTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatga                                                                                 <  2:60882/140‑1 (MQ=255)

                                         cTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatga                                                                                 <  1:510807/140‑1 (MQ=255)

                                               tGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCa                                                                           >  1:39291/1‑140 (MQ=255)

                                               tGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCa                                                                           >  1:635506/1‑140 (MQ=255)

                                                       tttaatttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTa                                                                   >  1:895106/1‑140 (MQ=255)

                                                           atttTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTaaaaa                                                               >  2:475954/1‑140 (MQ=255)

                                                               tACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaa                                                           >  2:1238674/1‑140 (MQ=255)

                                                                 cTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaaac                                                         <  1:475954/140‑1 (MQ=255)

                                                                 cTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAaaacaaac                                                         <  2:135194/140‑1 (MQ=255)

                                                                    aTGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAAt                                                      <  2:895106/140‑1 (MQ=255)

                                                                      gAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGa                                                    <  2:1113696/140‑1 (MQ=255)

                                                                         tAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa                                                 >  1:433430/1‑140 (MQ=255)

                                                                         tAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa                                                 >  2:222955/1‑140 (MQ=255)

                                                                              gTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATaa                                            >  1:1173704/1‑140 (MQ=255)

                                                                                aGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATg                                          <  2:975842/140‑1 (MQ=255)

                                                                                 gATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATg                                                     >  1:21760/1‑128 (MQ=255)

                                                                                 gATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATg                                                     <  2:21760/128‑1 (MQ=255)

                                                                                       attaatATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATg                                                     >  2:276506/1‑122 (MQ=255)

                                                                                       attaatATATTGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATg                                                     <  1:276506/122‑1 (MQ=255)

                                                                                                 tGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAAt                                           <  1:738892/122‑1 (MQ=255)

                                                                                                 tGATAGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAAt                                           >  2:738892/1‑122 (MQ=255)

                                                                                                     aGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                      <  2:115121/123‑1 (MQ=255)

                                                                                                     aGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGAt                                      >  1:115121/1‑123 (MQ=255)

                                                                                                     aGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAcc                           <  2:112895/134‑1 (MQ=255)

                                                                                                     aGGGGAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAcc                           >  1:112895/1‑134 (MQ=255)

                                                                                                       gggAAAGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTg                   >  2:884560/1‑140 (MQ=255)

                                                                                                          aaaGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCg                <  2:514665/140‑1 (MQ=255)

                                                                                                          aaaGATTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAACGCGATTGGCATTAACCCGCTTTTGTCg                >  2:259248/1‑140 (MQ=255)

                                                                                                              aTTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTTAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            <  2:512069/140‑1 (MQ=255)

                                                                                                              aTTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  >  1:1065611/1‑134 (MQ=255)

                                                                                                              aTTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  <  2:1065611/134‑1 (MQ=255)

                                                                                                              aTTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            <  1:1238674/140‑1 (MQ=255)

                                                                                                              aTTATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            <  2:544198/140‑1 (MQ=255)

                                                                                                               ttATCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGGACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatata           <  2:271001/140‑1 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  <  2:959027/131‑1 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  <  2:976091/131‑1 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  >  2:253465/1‑131 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  >  1:976091/1‑131 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  >  1:959027/1‑131 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGt                  <  1:253465/131‑1 (MQ=255)

                                                                                                                 aTCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatataat         >  2:670811/1‑140 (MQ=255)

                                                                                                                  tCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            <  2:557624/136‑1 (MQ=255)

                                                                                                                  tCTTAAGGAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            >  1:557624/1‑136 (MQ=255)

                                                                                                                        ggAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGatat            <  2:1223104/130‑1 (MQ=255)

                                                                                                                        ggAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAatatat     <  2:255355/137‑1 (MQ=255)

                                                                                                                        ggAACTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATaaa  >  1:792028/1‑140 (MQ=255)

AAATGTATTCGTTGGTGTGGGGTCGAATAGTGATGTTTTCACTCCCCTGATTCAATTTAATTTTACTAATGAGTAAATGTAGATTTAATTAATATATTGATAGGGGAAAGATTATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCCGCTTTTGTCGATATAATATATAAA  >  NC_000913/2455769‑2456028

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