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 I2 R1	760	67.6	3323148	92.7%	3080558	109.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,770,380	A→G	noncoding (9/106 nt)	rprA →	sRNA antisense activator for RpoS translation, Hfq‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,770,380	0	A	G	100.0%	188.4 / NA	53	noncoding (9/106 nt)	rprA	sRNA antisense activator for RpoS translation, Hfq‑dependent
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (31/22); total (31/22)

CTCTTCCCCATATTTTCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATAAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCACT  >  NC_000913/1770246‑1770511

ctctTCCCCATATTTTCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATc                                                                                                                                 >  1:1496114/1‑139 (MQ=255)

               tCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACata                                                                                                                           <  1:556880/130‑1 (MQ=255)

               tCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTtat                                                                                                                  >  2:1475988/1‑139 (MQ=255)

               tCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATGCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACata                                                                                                                           >  2:556880/1‑130 (MQ=255)

                 cTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATaa                                                                                                                >  1:1428105/1‑139 (MQ=255)

                    cTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCa                                                                                                             <  2:461645/139‑1 (MQ=255)

                    cTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCa                                                                                                             >  1:461645/1‑139 (MQ=255)

                    cTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCa                                                                                                             >  1:129090/1‑139 (MQ=255)

                      tACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATg                                                                                                           >  1:1508425/1‑139 (MQ=255)

                         cGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCa                                                                                                                                >  2:1250557/1‑115 (MQ=255)

                         cGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCa                                                                                                                                <  1:1250557/115‑1 (MQ=255)

                                   cTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          <  1:1087570/111‑1 (MQ=255)

                                   cTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          >  2:1087570/1‑111 (MQ=255)

                                   cTGGTAGTACCTGACGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          <  1:1368566/111‑1 (MQ=255)

                                   cTGGTAGTACCTGACGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          >  2:1368566/1‑111 (MQ=255)

                                          taCCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAaaca                                                                                       <  2:129090/139‑1 (MQ=255)

                                             cTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTtata                                                                                                                 >  1:1436158/1‑110 (MQ=255)

                                             cTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTtata                                                                                                                 <  2:1436158/110‑1 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          >  1:1186621/1‑98 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACatat                                                                                                                          <  2:1186621/98‑1 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAg                                                                                              >  1:1574692/1‑126 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAg                                                                                              <  2:1574692/126‑1 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAAt                                                                                 >  1:1554798/1‑139 (MQ=255)

                                                tCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAAt                                                                                 >  2:782931/1‑139 (MQ=255)

                                                 cGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCt                                                                                                 >  2:1017140/1‑122 (MQ=255)

                                                 cGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCt                                                                                                 <  1:1017140/122‑1 (MQ=255)

                                                 cGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAAtt                                                                                >  1:1436341/1‑139 (MQ=255)

                                                  gCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTg                                                                               <  2:1262594/139‑1 (MQ=255)

                                                  gCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTg                                                                               <  1:1475988/139‑1 (MQ=255)

                                                   cAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGc                                                                              <  1:601725/139‑1 (MQ=255)

                                                           ttACAGTTTTTAAACTAATGAGACGAATATGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTa                                                                      >  2:472911/1‑139 (MQ=255)

                                                                  ttttAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTtata                                                                                                                 <  1:693825/89‑1 (MQ=255)

                                                                  ttttAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTtata                                                                                                                 >  2:693825/1‑89 (MQ=255)

                                                                    ttAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGcc                                                             <  2:1508425/139‑1 (MQ=255)

                                                                     tAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGccc                                                            <  2:1519555/139‑1 (MQ=255)

                                                                           aaTGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTcc                                                      >  2:567937/1‑139 (MQ=255)

                                                                             tGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGATGTGTGTAGTCTTTGCCCATCTCCCa                                                    >  1:394587/1‑139 (MQ=255)

                                                                                 aCGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGAt                                                >  1:726354/1‑139 (MQ=255)

                                                                                          aTCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCt                                           <  2:1473776/135‑1 (MQ=255)

                                                                                          aTCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCt                                           >  1:1473776/1‑135 (MQ=255)

                                                                                               cGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTaa                                  >  2:1596602/1‑139 (MQ=255)

                                                                                                              tGCCTACTATTAGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCg                   <  2:1428105/139‑1 (MQ=255)

                                                                                                                         aGCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGccc        >  1:886295/1‑139 (MQ=255)

                                                                                                                          gCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGcccc       >  1:250458/1‑139 (MQ=255)

                                                                                                                          gCTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGcccc       >  1:1191570/1‑139 (MQ=255)

                                                                                                                           cTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCt      >  2:438153/1‑139 (MQ=255)

                                                                                                                           cTCACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCt      >  1:319827/1‑139 (MQ=255)

                                                                                                                             cACGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGTATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCa    <  2:394587/139‑1 (MQ=255)

                                                                                                                              aCGGTTATGAATCAACATATTGATTTATAAGCATGGaa                                                                                                        >  2:207207/1‑38 (MQ=255)

                                                                                                                              aCGGTTATGAATCAACATATTGATTTATAAGCATGGaa                                                                                                        <  1:207207/38‑1 (MQ=255)

                                                                                                                               cGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCAct  <  1:567937/139‑1 (MQ=255)

                                                                                                                               cGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCAct  >  1:336634/1‑139 (MQ=255)

                                                                                                                               cGGTTATGAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCAct  <  2:886295/139‑1 (MQ=255)

CTCTTCCCCATATTTTCCTGCTTACCGCCATTCAGCTGGTAGTACCTGTCGCAAATTCTTTACAGTTTTTAAACTAATGAGACGAATCTGATCGACGCAAAAAGTCCGTATGCCTACTATTAGCTCACGGTTATAAATCAACATATTGATTTATAAGCATGGAAATCCCCTGAGTGAAACAACGAATTGCTGTGTGTAGTCTTTGCCCATCTCCCACGATGGGCTTTTTTTTAACATTTTTCCGCTTCGCTACCTCGCCCCTCACT  >  NC_000913/1770246‑1770511

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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