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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,465,072	A→G	N384S (AAC→AGC)	gspL →	Type II secretion system protein GspL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,465,072	0	A	G	100.0%	178.9 / NA	50	N384S (AAC→AGC)	gspL	Type II secretion system protein GspL
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (25/25); total (25/25)

CGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATT  >  NC_000913/3464946‑3465204

cGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGa                                                                                                                          <  1:418825/140‑1 (MQ=255)

   tGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTa                                                                                                                       >  1:447077/1‑140 (MQ=255)

     aCCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTaaa                                                                                                                     <  1:291097/140‑1 (MQ=255)

        ttAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTaaa                                                                                                                     <  2:851072/137‑1 (MQ=255)

        ttAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTaaa                                                                                                                     >  1:851072/1‑137 (MQ=255)

                 aGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCa                                                                                                         <  2:447077/140‑1 (MQ=255)

                 aGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCa                                                                                                         >  1:812394/1‑140 (MQ=255)

                              aaGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACAt                                                                                            >  1:228165/1‑140 (MQ=255)

                               aGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACAt                                                                                            <  2:410264/139‑1 (MQ=255)

                               aGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACAt                                                                                            >  1:410264/1‑139 (MQ=255)

                               aGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATc                                                                                           <  2:228165/140‑1 (MQ=255)

                                          atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGa                                                                                >  2:613129/1‑140 (MQ=255)

                                          atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGa                                                                                >  1:790195/1‑140 (MQ=255)

                                          atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGa                                                                                >  2:812513/1‑140 (MQ=255)

                                          atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGa                                                                                >  1:214772/1‑140 (MQ=255)

                                           tcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGAt                                                                               <  2:361326/140‑1 (MQ=255)

                                             gTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCg                                                                             >  2:375385/1‑140 (MQ=255)

                                                                gTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAGAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTtct                                                          >  2:316102/1‑140 (MQ=255)

                                                                gTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCgg                                                              <  1:185230/136‑1 (MQ=255)

                                                                gTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCgg                                                              >  2:185230/1‑136 (MQ=255)

                                                                 tCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCAc                                                                    <  2:860401/129‑1 (MQ=255)

                                                                 tCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCAc                                                                    >  1:860401/1‑129 (MQ=255)

                                                                 tCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTtctc                                                         >  1:478896/1‑140 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCCCCCGGCg                                               >  2:792050/1‑140 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTctcgctc                                                   >  1:813482/1‑136 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTctcgctc                                                   <  2:813482/136‑1 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCg                                               >  2:150432/1‑140 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCg                                               >  1:478792/1‑140 (MQ=255)

                                                                           cGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCg                                               >  2:479335/1‑140 (MQ=255)

                                                                                  aaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTttg                                       <  1:792050/140‑1 (MQ=255)

                                                                                  aaaaaCAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTttg                                       <  2:351899/140‑1 (MQ=255)

                                                                                        aGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCt                                 <  2:478896/140‑1 (MQ=255)

                                                                                            aaaGATCCGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTggg                             <  1:479335/140‑1 (MQ=255)

                                                                                                   cGGTCAGTGGTGTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATaa                      <  2:812394/140‑1 (MQ=255)

                                                                                                         gtggtgTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCga                <  2:214772/140‑1 (MQ=255)

                                                                                                         gtggtgTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCga                <  1:613129/140‑1 (MQ=255)

                                                                                                           ggtgTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgata              <  2:478792/140‑1 (MQ=255)

                                                                                                           ggtgTATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgata              <  1:529411/140‑1 (MQ=255)

                                                                                                              gtATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgattgat           <  1:653458/140‑1 (MQ=255)

                                                                                                              gtATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgatagat           <  2:790195/140‑1 (MQ=255)

                                                                                                              gtATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgatagat           <  1:181881/140‑1 (MQ=255)

                                                                                                              gtATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCgatagat           <  1:312398/140‑1 (MQ=255)

                                                                                                               tATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCGGCG‑GTTTTTTTTGGGTTGGGGGGGTAAAAACgatagata          >  2:312398/1‑140 (MQ=255)

                                                                                                               tATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCTCCGCG‑GTTTTTTTTTGGTTGGGGGGGTAAAAACcatagata          >  2:181881/1‑140 (MQ=255)

                                                                                                               tATGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGGTCTCTCCCTCCGCGTTTTTTTTTTGGTTTGGGGGGGAAAAAccatttata           >  2:653458/1‑133 (MQ=255)

                                                                                                                aTGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATAc         <  1:292452/140‑1 (MQ=255)

                                                                                                                aTGGACAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATAc         <  1:150432/140‑1 (MQ=255)

                                                                                                                    aCAGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCCCTCGGCG‑GTTTTTTTTGGGTTGGGGGGGGAAAAACGATAGATACCCAc     >  2:589135/1‑140 (MQ=255)

                                                                                                                      aGTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCCCGGCG‑TTTTTTTTTGGGTTGGGGGGGTAAAAACGATAGATAACTACAt   >  1:464187/1‑140 (MQ=255)

                                                                                                                       gTAAGGAGCTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTTTCTCGCTCCGCG‑TTTTTTTTTGGCTTGGGGGGGTAAAAACGAGAGATACCTACAtt  >  2:292452/1‑140 (MQ=255)

CGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAGATCGTTGCGGCACTGGCGGTTCTCTCGCTCGGCG‑TTTTTTGTTGGCTTGGGGTGATAAAACCGATAGATACCTACATT  >  NC_000913/3464946‑3465204

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A