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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	578,568	G→A	154 (TAG→TAA)	rzpD →	DLP12 prophage, putative murein endopeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	578,568	0	G	A	100.0%	159.7 / NA	49	154 (TAG→TAA)	rzpD	DLP12 prophage, putative murein endopeptidase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (26/23); total (26/23)

GGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGT  >  NC_000913/578439‑578695

ggATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCa                                                                                                                        <  1:1131379/139‑1 (MQ=255)

           ccTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                             <  2:759447/139‑1 (MQ=255)

           ccTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                             <  2:1048447/139‑1 (MQ=255)

           ccTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                             >  2:149575/1‑139 (MQ=255)

            cTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCa                                                                                                            >  2:596141/1‑139 (MQ=255)

                  ccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCa                                                                                                                        <  1:137406/121‑1 (MQ=255)

                  ccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCa                                                                                                                        >  2:137406/1‑121 (MQ=255)

                       tGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                       <  1:937603/133‑1 (MQ=255)

                       tGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                       >  2:937603/1‑133 (MQ=255)

                         gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                  <  2:413408/136‑1 (MQ=255)

                         gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                  >  1:413408/1‑136 (MQ=255)

                                   cTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCaa                                                                                     >  2:92874/1‑139 (MQ=255)

                                         gggATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                               >  1:1062609/1‑139 (MQ=255)

                                                   cACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCa                                                                     <  1:149575/139‑1 (MQ=255)

                                                      ccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                  <  2:1062609/139‑1 (MQ=255)

                                                              agagGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                          <  1:92874/139‑1 (MQ=255)

                                                                agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCatat                                                                                                                     >  1:635084/1‑78 (MQ=255)

                                                                agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCatat                                                                                                                     <  2:635084/78‑1 (MQ=255)

                                                                    tGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCt                                                    >  2:966973/1‑139 (MQ=255)

                                                                      aTCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                  <  2:1018830/91‑1 (MQ=255)

                                                                      aTCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                  >  1:1018830/1‑91 (MQ=255)

                                                                                        cTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCaa                                >  1:520049/1‑139 (MQ=255)

                                                                                                aaCCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTa                        <  2:520049/139‑1 (MQ=255)

                                                                                                  cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               <  1:178930/130‑1 (MQ=255)

                                                                                                  cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               >  2:178930/1‑130 (MQ=255)

                                                                                                  cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACg                      >  2:329586/1‑139 (MQ=255)

                                                                                                          tataTTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               <  1:757923/122‑1 (MQ=255)

                                                                                                          tataTTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               >  2:757923/1‑122 (MQ=255)

                                                                                                            tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               <  1:14817/120‑1 (MQ=255)

                                                                                                            tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               >  2:14817/1‑120 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGc             <  1:873137/133‑1 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGc             >  2:873137/1‑133 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGtt       >  1:881840/1‑139 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGtt       >  1:308871/1‑139 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTACAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCt            <  1:877949/134‑1 (MQ=255)

                                                                                                                 aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTACAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCt            >  2:877949/1‑134 (MQ=255)

                                                                                                                    aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTg                                                                                          >  2:1017143/1‑53 (MQ=255)

                                                                                                                    aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTg                                                                                          <  1:1017143/53‑1 (MQ=255)

                                                                                                                    aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACAcgc                                                                            <  2:164365/67‑1 (MQ=255)

                                                                                                                    aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACAcgc                                                                            >  1:164365/1‑67 (MQ=255)

                                                                                                                      cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGt  >  1:597512/1‑139 (MQ=255)

                                                                                                                        gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               >  2:1033046/1‑108 (MQ=255)

                                                                                                                        gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                               <  1:1033046/108‑1 (MQ=255)

                                                                                                                         tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                  <  1:656514/88‑1 (MQ=255)

                                                                                                                         tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTATGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                  >  2:656514/1‑88 (MQ=255)

                                                                                                                           cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCa                                 <  2:494047/103‑1 (MQ=255)

                                                                                                                           cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCa                                 >  1:494047/1‑103 (MQ=255)

                                                                                                                              aTAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                    >  2:174158/1‑65 (MQ=255)

                                                                                                                              aTAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                    <  1:174158/65‑1 (MQ=255)

GGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGT  >  NC_000913/578439‑578695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A