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
A11 F1 I1 R1	757	76.1	3598070	93.4%	3360597	108.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,023,694	C→T	intergenic (+16/‑274)	fliR → / → rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,023,694	0	C	T	100.0%	158.3 / NA	49	intergenic (+16/‑274)	fliR/rcsA	flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (21/28); total (21/28)

CTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGA  >  NC_000913/2023560‑2023812

cTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGt                                                                                                                    <  2:184347/139‑1 (MQ=255)

cTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGt                                                                                                                    <  2:510991/139‑1 (MQ=255)

 tGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGtt                                                                                                                   <  1:1101725/139‑1 (MQ=255)

     ggCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATcc                                                                                                               >  2:459816/1‑139 (MQ=255)

         tctcTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAg                                                                                                           >  1:1011217/1‑139 (MQ=255)

                  tGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCg                                                                                                  <  1:459816/139‑1 (MQ=255)

                   ggcggcATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGa                                                                                                 <  2:615061/139‑1 (MQ=255)

                    gcggcATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     <  2:231699/118‑1 (MQ=255)

                    gcggcATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     >  1:231699/1‑118 (MQ=255)

                     cggcATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGaaa                                                                                               >  2:867349/1‑139 (MQ=255)

                              tGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGa                                                                                                 >  1:475667/1‑128 (MQ=255)

                              tGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGa                                                                                                 <  2:475667/128‑1 (MQ=255)

                                  gTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACg                                                                                  >  1:240602/1‑139 (MQ=255)

                                     aaTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAAc                                                                               <  2:240602/139‑1 (MQ=255)

                                      aTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACa                                                                              <  2:1011217/139‑1 (MQ=255)

                                      aTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACa                                                                              <  1:980520/139‑1 (MQ=255)

                                      aTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACa                                                                              <  1:867349/139‑1 (MQ=255)

                                           aCCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTc                                                                         <  1:1740569/139‑1 (MQ=255)

                                                tttGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGa                                                                    >  2:80328/1‑139 (MQ=255)

                                                tttGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGa                                                                    >  2:1481456/1‑139 (MQ=255)

                                                       aCATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     >  2:1747327/1‑83 (MQ=255)

                                                       aCATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     <  1:1747327/83‑1 (MQ=255)

                                                                   tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     >  2:500176/1‑71 (MQ=255)

                                                                   tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     <  1:500176/71‑1 (MQ=255)

                                                                   tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAatat                                                 >  2:970325/1‑139 (MQ=255)

                                                                         ttttAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTGATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGttt                                           <  1:628139/139‑1 (MQ=255)

                                                                             aaTTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                       <  1:1481456/139‑1 (MQ=255)

                                                                               tttGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGct                                     <  1:970325/139‑1 (MQ=255)

                                                                                   ctggctgATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcact                                 <  1:1477077/139‑1 (MQ=255)

                                                                                                ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACa                                                                              <  1:792950/81‑1 (MQ=255)

                                                                                                ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACa                                                                              >  2:792950/1‑81 (MQ=255)

                                                                                                ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGa                                                                    <  2:519249/91‑1 (MQ=255)

                                                                                                ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGa                                                                    >  1:519249/1‑91 (MQ=255)

                                                                                                    tGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     <  2:99002/38‑1 (MQ=255)

                                                                                                    tGAATTGCCATTAATATAATTCCGTAACGTTTATTATg                                                                                                                     >  1:99002/1‑38 (MQ=255)

                                                                                                    tGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAttt                >  2:188647/1‑139 (MQ=255)

                                                                                                        ttGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcac                                  <  1:834969/117‑1 (MQ=255)

                                                                                                        ttGCCATTAATATAATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcac                                  >  2:834969/1‑117 (MQ=255)

                                                                                                                  tataATTCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGa  <  1:151930/139‑1 (MQ=255)

                                                                                                                       ttCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcactc                                >  2:1795823/1‑104 (MQ=255)

                                                                                                                       ttCCGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcactc                                <  1:1795823/104‑1 (MQ=255)

                                                                                                                          cGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAatat                                                 <  1:949423/84‑1 (MQ=255)

                                                                                                                          cGTAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAatat                                                 >  2:949423/1‑84 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                       <  2:737663/92‑1 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                       >  1:737663/1‑92 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATc                         >  2:694373/1‑106 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATc                         <  1:694373/106‑1 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGa  >  2:329913/1‑129 (MQ=255)

                                                                                                                            tAACGTTTATTATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGa  <  1:329913/129‑1 (MQ=255)

CTGTCGGCATCTCTTTAATGGCGGCATTAATGCCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGA  >  NC_000913/2023560‑2023812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A