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 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,521,593	C→T	295 (TAG→TAA)	xapR ←	transcriptional activator of xapAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,521,593	0	C	T	100.0%	131.3 / NA	42	295 (TAG→TAA)	xapR	transcriptional activator of xapAB
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/19); total (23/19)

CCTGCACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521469‑2521726

ccTGCACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGc                                                                                                                         >  1:1155752/1‑139 (MQ=255)

         cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTa                                                                                                                                     <  1:1181702/118‑1 (MQ=255)

         cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAg                                                                                                                >  1:691660/1‑139 (MQ=255)

                         aGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                <  2:1032139/139‑1 (MQ=255)

                           cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                     <  2:573885/132‑1 (MQ=255)

                           cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                     >  1:573885/1‑132 (MQ=255)

                           cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  1:535544/1‑139 (MQ=255)

                           cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                              >  1:613/1‑139 (MQ=255)

                                     gcgcTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                    <  2:1155752/139‑1 (MQ=255)

                                          tttttGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTc                                                                               >  1:1278359/1‑139 (MQ=255)

                                                 tATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                        <  2:1278359/139‑1 (MQ=255)

                                                     tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACCACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                    >  1:922759/1‑139 (MQ=255)

                                                       cGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatatat                                                                  <  2:613/139‑1 (MQ=255)

                                                            tGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                                    <  2:988875/84‑1 (MQ=255)

                                                            tGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                                    >  1:988875/1‑84 (MQ=255)

                                                                        tGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATgcg                                                 >  2:426290/1‑139 (MQ=255)

                                                                                ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  1:137575/1‑106 (MQ=255)

                                                                                ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:137575/106‑1 (MQ=255)

                                                                                  cACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACCGCTTAACCATCGCGGGc                                                                                                <  2:856356/82‑1 (MQ=255)

                                                                                  cACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                                >  1:856356/1‑82 (MQ=255)

                                                                                     ttAGCAGACCACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcgga                                    <  2:922759/139‑1 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAGCTGCTGTGTTTCATaaa                                                                          >  1:979164/1‑94 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:979164/94‑1 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGc                                       >  1:1088264/1‑129 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGc                                       <  2:1088264/129‑1 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                             >  1:1302155/1‑139 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                             >  2:686258/1‑139 (MQ=255)

                                                                                            actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                             >  2:480572/1‑139 (MQ=255)

                                                                                             ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                            <  2:691660/139‑1 (MQ=255)

                                                                                             ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                            >  2:634980/1‑139 (MQ=255)

                                                                                              tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                                     >  1:450043/1‑49 (MQ=255)

                                                                                              tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                                     <  2:450043/49‑1 (MQ=255)

                                                                                                      ccGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgtg                                                                                   <  1:1271062/75‑1 (MQ=255)

                                                                                                      ccGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgtg                                                                                   >  2:1271062/1‑75 (MQ=255)

                                                                                                        ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 >  2:247024/1‑123 (MQ=255)

                                                                                                        ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGcggacgg                                 <  1:247024/123‑1 (MQ=255)

                                                                                                               ccTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCAt          <  2:178721/139‑1 (MQ=255)

                                                                                                                       ctcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             >  1:1172343/1‑64 (MQ=255)

                                                                                                                       ctcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCAt                                                                             <  2:1172343/64‑1 (MQ=255)

                                                                                                                       ctcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGt  >  1:240709/1‑139 (MQ=255)

                                                                                                                        tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          <  2:228135/66‑1 (MQ=255)

                                                                                                                        tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                          >  1:228135/1‑66 (MQ=255)

CCTGCACGACCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGT  >  NC_000913/2521469‑2521726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A