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	27	23.6	499472	97.1%	484987	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	58,444	G→T	intergenic (+890/+27)	USA300HOU_0048 → / ← USA300HOU_0049	hypothetical membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	58,444	0	G	T	100.0%	86.3 / NA	25	intergenic (+890/+27)	USA300HOU_0048/USA300HOU_0049	hypothetical membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (13/12); total (13/12)

CTTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACTTTT  >  CP000730/58306‑58580

ctTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACatat                                                                                                                                        >  1:88932/1‑141 (MQ=255)

 tttttAAAATCATCTAGTATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGTCTGGAAATTCAATGCTGTAAAATTAGACATAtt                                                                                                                                       >  1:294837/1‑141 (MQ=255)

  ttttAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAttt                                                                                                                                      >  1:397988/1‑141 (MQ=255)

  ttttAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAttt                                                                                                                                      >  1:32169/1‑141 (MQ=255)

            atcTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAagta                                                                                                                            >  1:132548/1‑141 (MQ=255)

                       tatataATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAg                                                                                                                 <  1:317905/141‑1 (MQ=255)

                              ttCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATAGTTTAAAAAAGTAGTAATAAAAAGTCTAAGt                                                                                                          >  1:81501/1‑141 (MQ=255)

                                            gtaTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaat                                                                                            <  1:315239/141‑1 (MQ=255)

                                              aTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:437050/141‑1 (MQ=255)

                                              aTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:108192/141‑1 (MQ=255)

                                              aTTAACCTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                          <  1:108017/141‑1 (MQ=255)

                                                tAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAAc                                                                                        >  1:380518/1‑141 (MQ=255)

                                                tAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAAc                                                                                        >  1:229973/1‑141 (MQ=255)

                                                    gTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTca                                                                                    >  1:498665/1‑140 (MQ=255)

                                                                       aaaTATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAAGTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAaaataaat                                                                 <  1:36558/141‑1 (MQ=255)

                                                                           atTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAGTAAATATGa                                                             >  1:6621/1‑141 (MQ=255)

                                                                                         tAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAtttt                                               <  1:357699/141‑1 (MQ=255)

                                                                                               ttgaaaTTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCCTTTAATTTCTataa                                         <  1:270831/138‑1 (MQ=255)

                                                                                                       ataCGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAATGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAg                                 <  1:198190/141‑1 (MQ=255)

                                                                                                       ataCGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAg                                 >  1:282798/1‑141 (MQ=255)

                                                                                                                  aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGa                      >  1:459179/1‑141 (MQ=255)

                                                                                                                  aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGa                      >  1:241591/1‑141 (MQ=255)

                                                                                                                    tttaaTGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGAtt                    <  1:469649/138‑1 (MQ=255)

                                                                                                                    ttCAATGCTTTAAAAATAGACATATTTTAAAAAAGTAGTAATAAATAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGAtt                    <  1:464777/141‑1 (MQ=255)

                                                                                                                              tAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTg          <  1:77647/141‑1 (MQ=255)

                                                                                                                                      gACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACtttt  >  1:451586/1‑141 (MQ=255)

CTTTTTAAAATCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAACTTTT  >  CP000730/58306‑58580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A