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
A15 F177 I1 R2	35	38.3	831348	95.5%	793937	139.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,388,866	A→G	G8G (GGA→GGG)	USA300HOU_2249 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,388,866	0	A	G	100.0%	110.6 / NA	32	G8G (GGA→GGG)	USA300HOU_2249	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/16); total (16/16)

TCCTATGTTTCTTCTTAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGACAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTCTTAAGAGTGGGATAGAAAT  >  CP000730/2388729‑2389000

tcctATGTTTCTTCTTAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCaa                                                                                                                                     <  1:250557/141‑1 (MQ=255)

     tGTTTCTTCTTAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACttgt                                                                                                                                <  2:50033/141‑1 (MQ=255)

         tcttctTAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTgttgtt                                                                                                                            >  1:55533/1‑141 (MQ=255)

          cttcttAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGttt                                                                                                                           <  1:296862/141‑1 (MQ=255)

               tAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCg                                                                                                                      >  2:20082/1‑141 (MQ=255)

                  aTGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTTGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGaca                                                                                                                   >  1:262920/1‑141 (MQ=255)

                   tGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGacaa                                                                                                                  <  2:276764/141‑1 (MQ=255)

                    gTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGacaac                                                                                                                 >  2:173487/1‑141 (MQ=255)

                           aTTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTtata                                                                                                          <  1:360779/141‑1 (MQ=255)

                            ttCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATAc                                                                                                         <  1:249062/141‑1 (MQ=255)

                              cATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCt                                                                                                       >  2:113909/1‑141 (MQ=255)

                                 attattatACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTaaa                                                                                                    <  1:312804/141‑1 (MQ=255)

                                                     aTTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCaa                                                                                >  1:414269/1‑141 (MQ=255)

                                                         attatATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGc                                                                            <  2:174503/141‑1 (MQ=255)

                                                          ttatATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCa                                                                           >  2:327561/1‑141 (MQ=255)

                                                            atatatCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATg                                                                         >  1:275446/1‑141 (MQ=255)

                                                              atatCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGa                                                                       <  1:99374/141‑1 (MQ=255)

                                                              atatCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGa                                                                       <  1:412484/141‑1 (MQ=255)

                                                               tatCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAg                                                                      >  2:361338/1‑141 (MQ=255)

                                                                           cATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAAt                                                          >  2:352472/1‑141 (MQ=255)

                                                                             ttttATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGt                                                        >  2:173179/1‑141 (MQ=255)

                                                                                          aaaTATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTa                                           <  1:195154/141‑1 (MQ=255)

                                                                                           aaTATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTaa                                          <  1:20082/141‑1 (MQ=255)

                                                                                               ttAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGAt                                      >  1:45238/1‑141 (MQ=255)

                                                                                                        tGGCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAAGATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGt                             >  2:405823/1‑141 (MQ=255)

                                                                                                          gCTATATCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAg                           <  2:272222/141‑1 (MQ=255)

                                                                                                                tCTTGTTTAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTc                     <  1:173487/141‑1 (MQ=255)

                                                                                                                     tttAGATTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTCTTAag                >  1:173929/1‑141 (MQ=255)

                                                                                                                          aTTTATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGCACCACTAAAGATTTATTATGTAGTGATTCTTAAGAGTgg           <  2:246838/141‑1 (MQ=255)

                                                                                                                           tttATATATTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACACCTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTCAAGATTTATTATGTAGTGATTCTTAAGAGTggg          <  1:163226/141‑1 (MQ=255)

                                                                                                                                atatTTTGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTCTTAAGAGTGGGATAGa     >  2:343559/1‑141 (MQ=255)

                                                                                                                                   ttttGGGCAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTCTTAAGAGTGGGATAGAAAt  >  2:32622/1‑141 (MQ=255)

TCCTATGTTTCTTCTTAGATGTTTGTAATTCATATTATTATACAATTACTTAAATTTATTATATATCAAACTTAGCATTTTATCTATTACAAATATTAAATTGCTGGCTATATCTTGTTTAGATTTATATATTTTGGACAACTTGTTGTTTATTCGACAACATTTATACCTAAAAAAGATATATTACAACTCAATGGCATGGAGTGTGACATCAATGTTAAAGAACCACTAAAGATTTATTATGTAGTGATTCTTAAGAGTGGGATAGAAAT  >  CP000730/2388729‑2389000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A