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 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,039,654	(C)_5→4	coding (177/1005 nt)	yedY →	membrane‑anchored, periplasmic TMAO, DMSO reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,039,650	0	C	.	100.0%	157.1 / NA	38	coding (173/1005 nt)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (21/17); total (21/17)

CCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCT  >  NC_000913/2039518‑2039783

ccGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGcccgccccgcc                                                                                                                                 >  2:1418165/1‑136 (MQ=255)

   aGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGa                                                                                                                             >  2:317066/1‑139 (MQ=255)

              tttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGa                                                                                                                  >  2:441539/1‑139 (MQ=255)

              tttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGa                                                                                                                  >  1:744606/1‑139 (MQ=255)

               ttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAg                                                                                                                 <  2:744606/139‑1 (MQ=255)

                tATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGt                                                                                                                >  1:570144/1‑139 (MQ=255)

                 aTGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGtt                                                                                                               >  2:689134/1‑139 (MQ=255)

                      gCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCa                                                                                                          <  2:460603/139‑1 (MQ=255)

                       cGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCaa                                                                                                         >  1:614208/1‑139 (MQ=255)

                        gTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAg                                                                                                        >  1:321548/1‑139 (MQ=255)

                          cGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGcc                                                                                                      >  1:639192/1‑139 (MQ=255)

                                gtgtTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTgccgc                                                                                                >  2:715127/1‑139 (MQ=255)

                                  gtTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              <  1:317066/139‑1 (MQ=255)

                                           aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  2:1313719/1‑139 (MQ=255)

                                           aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  2:1079459/1‑139 (MQ=255)

                                           aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa                                                                                     >  1:953319/1‑139 (MQ=255)

                                             tGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAAc                                                                                   >  2:237255/1‑139 (MQ=255)

                                                         cAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACg                                                                       >  2:496610/1‑139 (MQ=255)

                                                           aCTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGcc                                                                     <  1:689134/139‑1 (MQ=255)

                                                            cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    <  1:715127/139‑1 (MQ=255)

                                                            cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    >  2:1148416/1‑139 (MQ=255)

                                                            cTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGATGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCAGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCca                                                                    <  1:956584/139‑1 (MQ=255)

                                                                  tttctttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGAt                                                              <  1:441539/139‑1 (MQ=255)

                                                                      tttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATcgcccgcccgc                                                                                                                                       >  1:233390/1‑63 (MQ=255)

                                                                      tttGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATcgcccgcccgc                                                                                                                                       <  2:233390/63‑1 (MQ=255)

                                                                         gCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGttt                                                       <  2:639192/139‑1 (MQ=255)

                                                                             cACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCgg                                                   <  1:1418165/139‑1 (MQ=255)

                                                                              aCGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGt                                                  >  2:745482/1‑139 (MQ=255)

                                                                                    cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTc                                                      >  2:1454014/1‑129 (MQ=255)

                                                                                    cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTc                                                      <  1:1454014/129‑1 (MQ=255)

                                                                                    cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataat                                            <  1:1313719/139‑1 (MQ=255)

                                                                                    cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataat                                            <  1:1259597/139‑1 (MQ=255)

                                                                                          ccGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              <  2:270354/83‑1 (MQ=255)

                                                                                          ccGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt                                                                                              >  1:270354/1‑83 (MQ=255)

                                                                                                      gCTGGTTTAAATGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg                          <  2:953319/139‑1 (MQ=255)

                                                                                                      gCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg                          <  2:614208/139‑1 (MQ=255)

                                                                                                            ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg                                                    >  2:334864/1‑107 (MQ=255)

                                                                                                            ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg                                                    <  1:334864/107‑1 (MQ=255)

                                                                                                                 gggAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGc               >  1:1475508/1‑139 (MQ=255)

                                                                                                                        aTCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATccc        <  2:1361848/139‑1 (MQ=255)

                                                                                                                         tCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCccg       >  2:1165849/1‑139 (MQ=255)

                                                                                                                           gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCccgcc     >  2:875307/1‑139 (MQ=255)

                                                                                                                              cgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCt  >  1:484472/1‑139 (MQ=255)

CCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCCCGCCGCT  >  NC_000913/2039518‑2039783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A