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 F67 I1 R1	28	23.6	502806	98.6%	495766	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,652	C→T	intergenic (‑8/+7)	USA300HOU_RS10230 ← / ← USA300HOU_RS10235	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,652	0	C	T	100.0%	83.9 / NA	25	intergenic (‑8/+7)	USA300HOU_RS10230/USA300HOU_RS10235	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (14/11); total (14/11)

CACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAACTCTGATTT  >  USA300TCH1516_ALE/2028521‑2028787

cacaTCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTa                                                                                                                                >  1:84494/1‑141 (MQ=255)

    tCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGcc                                                                                                                            <  1:262735/141‑1 (MQ=255)

      ccAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTTCCTTTCTATGCcac                                                                                                                          >  1:121859/1‑141 (MQ=255)

      ccAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCcac                                                                                                                          >  1:130996/1‑141 (MQ=255)

       cAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCcaca                                                                                                                         >  1:98224/1‑141 (MQ=255)

                aaCGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCCATTGTCTGCTATGCCACAGCGTTCata                                                                                                                <  1:119776/141‑1 (MQ=255)

                     gTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAAtt                                                                                                           <  1:89826/141‑1 (MQ=255)

                       aaaaaGCCAATTTTTTCAAACAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAAtttt                                                                                                         >  1:304868/1‑140 (MQ=255)

                       aaaaaGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATtta                                                                                                         >  1:163250/1‑141 (MQ=255)

                                        aaaaaaTATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGttttt                                                                                        >  1:16955/1‑141 (MQ=255)

                                                 gtagtaAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCGTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCt                                                                               <  1:42353/141‑1 (MQ=255)

                                                       aaaaTTGGCAATAATCCTTAAGTGTTG‑AAAAAGGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTAttttt                                                                         <  1:212447/141‑1 (MQ=255)

                                                                 ataatCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAg                                                               <  1:264672/141‑1 (MQ=255)

                                                                  taatCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTGTTTCTGTTGCTATTTTTTCAGTTGAAGt                                                              <  1:317567/141‑1 (MQ=255)

                                                                                  tAAAAATTGTCAACCTTGGCGTGGATATTTATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               <  1:108296/141‑1 (MQ=255)

                                                                                  tAAAAATGATCAACATTTGCGTTGATATCTATTTGTGTGTCCTGTTGCGCTGCCTTTCTATGCCACCACGTATAAATATTTTCTTCGACGCTTTGGTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               <  1:366481/141‑1 (MQ=255)

                                                                                  tAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGt                                               >  1:177849/1‑141 (MQ=255)

                                                                                     aaaTGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTc                                            >  1:106426/1‑141 (MQ=255)

                                                                                     aaaTGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTc                                            >  1:157727/1‑141 (MQ=255)

                                                                                         gATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAAtt                                        >  1:387144/1‑141 (MQ=255)

                                                                                         gATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAAtt                                        >  1:188175/1‑141 (MQ=255)

                                                                                           tCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTtg                                      >  1:27229/1‑141 (MQ=255)

                                                                                                aTTTGCGTTGATATATATTTGTGTGTCATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGCTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCat                                 <  1:331093/141‑1 (MQ=255)

                                                                                                       ttGATATATATTTGTGTGTCATATTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGATTGTTGAATTTGAGTTTCAATTTGTGCATAATATGc                          <  1:346426/141‑1 (MQ=255)

                                                                                                                          cATGTTTCGCTGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAActct       >  1:281270/1‑141 (MQ=255)

                                                                                                                               tccgctgcCTTTCTATGCCACGTCTTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTCTATTCAACTCTGAttt  <  1:256391/139‑1 (MQ=255)

CACATCCCAATAATAGAACGAGTAAAAAGCCAATTTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAA‑TGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCAGTTGAAGTTTGTTGAATTTGAGTTTCAATTTGTGCATAATATGCTTCAACTTTATTCAACTCTGATTT  >  USA300TCH1516_ALE/2028521‑2028787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A