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 I1 R1	759	71.0	3673240	91.5%	3361014	104.6

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%	201.4 / NA	63	154 (TAG→TAA)	rzpD	DLP12 prophage, putative murein endopeptidase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (30/33); total (30/33)

CAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTT  >  NC_000913/578447‑578698

cAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATg                                                                                                                   <  2:1129039/139‑1 (MQ=255)

    cTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCa                                                                                                               <  1:288759/139‑1 (MQ=255)

        ccccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTc                                                                                                           >  1:1330424/1‑139 (MQ=255)

         cccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                          <  2:927036/139‑1 (MQ=255)

         cccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                          <  2:353242/139‑1 (MQ=255)

                 gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGGACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                >  2:1482911/1‑109 (MQ=255)

                 gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGGACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                <  1:1482911/109‑1 (MQ=255)

                        ccGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           >  2:229877/1‑139 (MQ=255)

                        ccGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:1330424/139‑1 (MQ=255)

                           cTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCaa                                                                                        >  2:1332853/1‑139 (MQ=255)

                               aCGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATaca                                                                                    <  1:1332853/139‑1 (MQ=255)

                                            ccccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  1:1005212/138‑1 (MQ=255)

                                              ccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     <  1:161044/139‑1 (MQ=255)

                                                  agagagagGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGt                                                                 >  1:807481/1‑139 (MQ=255)

                                                        agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                     >  1:825330/1‑97 (MQ=255)

                                                        agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                     <  2:825330/97‑1 (MQ=255)

                                                        agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           >  1:1648635/1‑107 (MQ=255)

                                                        agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:1648635/107‑1 (MQ=255)

                                                          gCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     <  1:1406109/127‑1 (MQ=255)

                                                          gCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     >  2:1406109/1‑127 (MQ=255)

                                                           cTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        <  1:229877/139‑1 (MQ=255)

                                                                    aTGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                <  1:1553124/90‑1 (MQ=255)

                                                                    aTGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                >  2:1553124/1‑90 (MQ=255)

                                                                          aaaCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAAcc                                         >  1:731751/1‑139 (MQ=255)

                                                                               acTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCa                                                                                         >  1:1424264/1‑86 (MQ=255)

                                                                               acTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCa                                                                                         <  2:1424264/86‑1 (MQ=255)

                                                                                cTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTAtttt                                                                                              <  2:637958/80‑1 (MQ=255)

                                                                                cTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTAtttt                                                                                              >  1:637958/1‑80 (MQ=255)

                                                                                cTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCaa                                   >  2:1313338/1‑139 (MQ=255)

                                                                                 tGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  <  2:807481/139‑1 (MQ=255)

                                                                                   gaaggaaCCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATcc                                <  2:731751/139‑1 (MQ=255)

                                                                                          cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  1:699068/73‑1 (MQ=255)

                                                                                          cccAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           >  2:699068/1‑73 (MQ=255)

                                                                                                    tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             <  2:1652938/93‑1 (MQ=255)

                                                                                                    tatTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             >  1:1652938/1‑93 (MQ=255)

                                                                                                         aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATTCACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGtt          <  1:1313338/139‑1 (MQ=255)

                                                                                                         aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       >  2:818744/1‑78 (MQ=255)

                                                                                                         aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  1:818744/78‑1 (MQ=255)

                                                                                                         aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  <  1:1768354/115‑1 (MQ=255)

                                                                                                         aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  >  2:1768354/1‑115 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCaa                                                                                        >  2:1284271/1‑58 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCaa                                                                                        <  1:1284271/58‑1 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATaaaa                                           >  2:111785/1‑103 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATaaaa                                           <  1:111785/103‑1 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCt       >  2:900089/1‑139 (MQ=255)

                                                                                                            aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCt       >  1:1593683/1‑139 (MQ=255)

                                                                                                              cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           >  1:480794/1‑53 (MQ=255)

                                                                                                              cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:480794/53‑1 (MQ=255)

                                                                                                                gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  2:454613/71‑1 (MQ=255)

                                                                                                                gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGttt   <  2:1593683/139‑1 (MQ=255)

                                                                                                                gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGttt   >  2:857371/1‑139 (MQ=255)

                                                                                                                gTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTACTTTGAGCAATACACACGCGCTTCCAg                                                                       >  1:454613/1‑71 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  <  1:170770/59‑1 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  >  2:170770/1‑59 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        >  1:1301657/1‑85 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        <  2:1301657/85‑1 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCt               >  2:306551/1‑126 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCt               <  1:306551/126‑1 (MQ=255)

                                                                                                                 tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGtttt  >  2:1066059/1‑139 (MQ=255)

                                                                                                                   cAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                     >  2:1607743/1‑38 (MQ=255)

                                                                                                                   cAGATAAAGCTGACCATATCGATGGGCAACTCATGCaa                                                                                                     <  1:1607743/38‑1 (MQ=255)

                                                                                                                   cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     >  2:104776/1‑86 (MQ=255)

                                                                                                                   cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     <  1:104776/86‑1 (MQ=255)

CAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTT  >  NC_000913/578447‑578698

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