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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

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%	169.6 / NA	53	154 (TAG→TAA)	rzpD	DLP12 prophage, putative murein endopeptidase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (26/27); total (26/27)

GGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAA  >  NC_000913/578434‑578700

ggCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                  <  1:402976/139‑1 (MQ=255)

     ggATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCa                                                                                                                             >  1:46587/1‑139 (MQ=255)

           tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                       >  2:1066382/1‑139 (MQ=255)

           tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                       <  1:385718/139‑1 (MQ=255)

           tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCACTGCAGATAAAGCTGACCAGATCGa                                                                                                                       <  2:280017/139‑1 (MQ=255)

                ccTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAGACCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTCCAGATAAGGCTGACCATATCGCTGGGc                                                                                                                  >  2:639034/1‑139 (MQ=37)

                      cccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                            <  2:203618/139‑1 (MQ=255)

                                  acacCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTAtttt                                                                                                <  2:46587/139‑1 (MQ=255)

                                           aaCGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                  >  2:154413/1‑128 (MQ=255)

                                           aaCGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                  <  1:154413/128‑1 (MQ=255)

                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                       >  1:41041/1‑92 (MQ=255)

                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                       <  2:41041/92‑1 (MQ=255)

                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCa                                                                                           <  2:373787/120‑1 (MQ=255)

                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCa                                                                                           >  1:373787/1‑120 (MQ=255)

                                                               agagagagGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGt                                                                   >  2:712868/1‑139 (MQ=255)

                                                                     agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAAt                                                             >  1:1051578/1‑139 (MQ=255)

                                                                     agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAAt                                                             >  2:492615/1‑139 (MQ=255)

                                                                           aTCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                       <  2:1051578/139‑1 (MQ=255)

                                                                             cACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                         <  1:465063/119‑1 (MQ=255)

                                                                             cACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                         >  2:465063/1‑119 (MQ=255)

                                                                                 aTGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGtaat                                                 >  1:362880/1‑139 (MQ=255)

                                                                                  tGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                  >  2:261132/1‑57 (MQ=255)

                                                                                  tGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                  <  1:261132/57‑1 (MQ=255)

                                                                                  tGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGtaata                                                >  1:899088/1‑139 (MQ=255)

                                                                                            acTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                       <  1:109727/122‑1 (MQ=255)

                                                                                            acTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                       >  2:109727/1‑122 (MQ=255)

                                                                                            acTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCa                                      <  1:1066382/139‑1 (MQ=255)

                                                                                              tGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                    <  1:492615/139‑1 (MQ=255)

                                                                                                     aaCCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                                  <  1:369126/54‑1 (MQ=255)

                                                                                                     aaCCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                                  >  2:369126/1‑54 (MQ=255)

                                                                                                       cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                             <  1:944249/73‑1 (MQ=255)

                                                                                                       cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                             >  2:944249/1‑73 (MQ=255)

                                                                                                          aGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATcc                                  <  2:520011/129‑1 (MQ=255)

                                                                                                          aGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATcc                                  >  1:520011/1‑129 (MQ=255)

                                                                                                               tataTTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTg                   <  1:648005/139‑1 (MQ=255)

                                                                                                                 tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATg                       <  2:1090088/133‑1 (MQ=255)

                                                                                                                 tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATg                       >  1:1090088/1‑133 (MQ=255)

                                                                                                                 tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGc                  <  1:146823/138‑1 (MQ=255)

                                                                                                                 tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGc                  >  2:146823/1‑138 (MQ=255)

                                                                                                                      aTGAGCAGTGCAGATAAAGCTGACCATAACGATGAGCAACTCATCCAATTATTTTCAGCAAAACACACGCGCTTACAGCGGAGTATAAATCCCTAAAATAATAAAACCGAGCAATCAACATACGAATGTTTGCTGGGtt            >  2:70048/1‑139 (MQ=255)

                                                                                                                       tGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                       <  2:274212/47‑1 (MQ=255)

                                                                                                                       tGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                       >  1:274212/1‑47 (MQ=255)

                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCATTTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                       >  2:787471/1‑93 (MQ=255)

                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                         >  2:85968/1‑75 (MQ=255)

                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                         <  1:85968/75‑1 (MQ=255)

                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                       <  1:787471/93‑1 (MQ=255)

                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATaca                                                                                      >  2:412032/1‑60 (MQ=255)

                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATaca                                                                                      <  1:412032/60‑1 (MQ=255)

                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGtaa                                                  <  1:464172/93‑1 (MQ=255)

                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGtaa                                                  >  2:464172/1‑93 (MQ=255)

                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCaa                                     >  1:632057/1‑106 (MQ=255)

                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCaa                                     <  2:632057/106‑1 (MQ=255)

                                                                                                                                cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTaa  <  2:899088/139‑1 (MQ=255)

GGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAA  >  NC_000913/578434‑578700

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