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
A7 F1 I2 R1	94	59.5	3027142	91.9%	2781943	108.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,926	(C)_6→7	coding (828/1140 nt)	nlpD ←	activator of AmiC murein hydrolase activity, lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,920	1	.	C	100.0%	189.7 / NA	53	G278G (GGC→GGG)	nlpD	activator of AmiC murein hydrolase activity, lipoprotein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (28/25); total (28/25)

TCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑CCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGTGCTTGCTGTTGGTACCGTTACAGG  >  NC_000913/2867784‑2868051

tCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑cc                                                                                                                                   >  2:169632/1‑139 (MQ=255)

          atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGa                                                                                                                          <  2:93298/139‑1 (MQ=255)

            catTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAg                                                                                                                        >  1:1101777/1‑139 (MQ=255)

                    ttGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAg                                                                                                                >  1:936402/1‑139 (MQ=255)

                    ttGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAg                                                                                                                <  1:136766/139‑1 (MQ=255)

                      gatgatAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGt                                                                                                              >  2:1115057/1‑139 (MQ=255)

                             aTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATc                                                                                                       <  1:1115057/139‑1 (MQ=255)

                             aTCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATc                                                                                                       >  2:45542/1‑139 (MQ=255)

                                    tACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGc                                                                                                >  1:71142/1‑139 (MQ=255)

                                     aCCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGcc                                                                                               <  2:1101777/139‑1 (MQ=255)

                                         tAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCa                                                                                           >  1:1373533/1‑139 (MQ=255)

                                         tAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCa                                                                                           >  2:213677/1‑139 (MQ=255)

                                            ccGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTc                                                                                        >  1:895424/1‑139 (MQ=255)

                                            ccGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTc                                                                                        >  2:1417365/1‑139 (MQ=255)

                                            ccGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTc                                                                                        >  1:1168199/1‑139 (MQ=255)

                                            ccGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTc                                                                                        >  2:1511050/1‑139 (MQ=255)

                                                gcAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATcgct                                                                                                    >  1:1004869/1‑120 (MQ=255)

                                                gcAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCGCt                                                                                                    <  2:596004/123‑1 (MQ=255)

                                                gcAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCGCt                                                                                                    <  2:1004869/123‑1 (MQ=255)

                                                gcAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCGCt                                                                                                    >  1:596004/1‑123 (MQ=255)

                                                 cAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCa                                                                                   >  1:1390949/1‑139 (MQ=255)

                                                    cgcgTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCa                                                                                   <  2:69182/136‑1 (MQ=255)

                                                    cgcgTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCa                                                                                   >  1:69182/1‑136 (MQ=255)

                                                      cgTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGcc                                                                              >  2:385865/1‑139 (MQ=255)

                                                         tACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTTCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAgg                                                                           <  2:914116/139‑1 (MQ=255)

                                                             aGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGga                                                                       <  2:1168199/139‑1 (MQ=255)

                                                              gCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGgag                                                                      >  2:983695/1‑139 (MQ=255)

                                                                  aaaCAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAg                                                                  <  2:1390949/139‑1 (MQ=255)

                                                                       acGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTa                                                             <  1:1511050/139‑1 (MQ=255)

                                                                       acGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTa                                                             <  2:895424/139‑1 (MQ=255)

                                                                       acGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTa                                                             <  2:1373533/139‑1 (MQ=255)

                                                                        cgcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAgcg                                                                                <  1:1322081/119‑1 (MQ=255)

                                                                        cgcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAgcg                                                                                >  2:1322081/1‑119 (MQ=255)

                                                                         gcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑ccc                                                                                                                                  >  1:131633/1‑67 (MQ=255)

                                                                         gcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑ccc                                                                                                                                  <  2:131633/67‑1 (MQ=255)

                                                                         gcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑c                                                                                                                                    <  1:593061/65‑1 (MQ=255)

                                                                         gcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑c                                                                                                                                    >  2:593061/1‑65 (MQ=255)

                                                                         gcgGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCCGCGATATCAATCCCCTTGTGGCCCCCCCTCAGAAGCGCCAGAGGTTTCGATCACTTTGCCCTCAGTCTGCCAGCGCCAGGTGGAGATAGGCGTACt                                                           <  1:933150/139‑1 (MQ=255)

                                                                           ggCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTgg                                                         <  1:1417365/139‑1 (MQ=255)

                                                                            gCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGt                                                        <  2:71142/139‑1 (MQ=255)

                                                                             ccATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGtt                                                       >  2:1301273/1‑139 (MQ=255)

                                                                                  tGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGt                                                  <  1:45542/139‑1 (MQ=255)

                                                                                      gTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGa                                                                                                         <  1:207852/80‑1 (MQ=255)

                                                                                      gTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGa                                                                                                         >  2:207852/1‑80 (MQ=255)

                                                                                          cgATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGa                                          >  2:386750/1‑139 (MQ=255)

                                                                                                       tCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGcc                                                                                    <  1:243813/84‑1 (MQ=255)

                                                                                                       tCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGcc                                                                                    >  2:243813/1‑84 (MQ=255)

                                                                                                       tCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGc                                                                                     <  2:289747/83‑1 (MQ=255)

                                                                                                       tCCTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGc                                                                                     >  1:289747/1‑83 (MQ=255)

                                                                                                        ccTTTGCTGCCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGtt                            <  1:386750/139‑1 (MQ=255)

                                                                                                             gctgcCTGCGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGtgct                       >  1:1056456/1‑139 (MQ=255)

                                                                                                                    gcGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCt                                 <  1:1483612/122‑1 (MQ=255)

                                                                                                                    gcGATATCAATCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCt                                 >  2:1483612/1‑122 (MQ=255)

                                                                                                                        ttgataTCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAgcg                                                                                >  2:1250077/6‑71 (MQ=255)

                                                                                                                        ttgataTCCCCTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAgcg                                                                                <  1:1250077/66‑1 (MQ=255)

                                                                                                                                cccTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGTGCTTGCTGTTGGTACCGTTACa    <  1:1301273/139‑1 (MQ=255)

                                                                                                                                  cTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGTGCTTGCTGTTGGTACCGTTACAgg  >  2:117981/1‑139 (MQ=255)

                                                                                                                                  cTTGTTGCCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGTGCTTGCTGTTGGTACCGTTACAgg  >  1:295974/1‑139 (MQ=255)

                                                                                                                                    tgttgcCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGtgctt                      >  2:402106/1‑117 (MQ=255)

                                                                                                                                    tgttgcCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGtgctt                      <  1:402106/117‑1 (MQ=255)

                                                                                                                                    tgttgcCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGtgc                        <  2:68307/115‑1 (MQ=255)

                                                                                                                                    tgttgcCCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGtgc                        >  1:68307/1‑115 (MQ=255)

TCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGCGATAATTGCCTGTCCTTTGCTGCCTGCGATATCAATCCCCTTGTTG‑CCCCCCTCAGAAGCGCCAAAGGTTTCGATCACTTTGCCCTCAGTCGGCCAGCGCCAGGTGGAGATAGGCGTACTGGTTGATGTACTGCTGACAGTCGGCTCGGTTGTGCTTGCTGTTGGTACCGTTACAGG  >  NC_000913/2867784‑2868051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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