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
A5 F109 I1 R1	27	23.1	511165	92.8%	474361	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	92.3%	66.6 / ‑5.9	26	intergenic (+890/+27)	USA300HOU_0048/USA300HOU_0049	hypothetical membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (12/12); minor base A (0/2); total (12/14)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAA  >  CP000730/58316‑58575

tcatcTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTaaaaaaa                                                                                                                         >  2:260679/1‑140 (MQ=255)

     tAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGCAATATTTTAAAAAAgtagta                                                                                                                    >  2:392183/1‑141 (MQ=255)

               tataATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTc                                                                                                          >  2:239943/1‑141 (MQ=255)

                     ttaattaatgggagtaTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGtt                                                                                                    <  2:217256/129‑1 (MQ=255)

                         ataAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTAt                                                                                                >  2:77647/1‑141 (MQ=255)

                                    aTTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGtaataa                                                                                     <  2:345438/141‑1 (MQ=255)

                                     ttAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATaaa                                                                                    <  2:211780/141‑1 (MQ=255)

                                        aCGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACtt                                                                                 >  2:26869/1‑141 (MQ=255)

                                         cGTTTTCTACTTTATCTATAAAATATTTGGAATTACATTAGAATTTTAAATTATACGGCTGAAAATTCAATGAAGTAAAAATAGACATATGCTAAAAAATTAGTAATAAAAAGTCTAAGTATTATCTTGGtttaacacttt                                                                                >  2:173062/1‑131 (MQ=255)

                                                             aaaTATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAaaataaat                                                            <  2:397988/141‑1 (MQ=255)

                                                             aaaTATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAaaataaat                                                            <  2:32169/141‑1 (MQ=255)

                                                              aaTATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAaataaata                                                           >  2:472828/1‑141 (MQ=255)

                                                                tatTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATg                                                         >  2:357699/1‑141 (MQ=255)

                                                                      gAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTc                                                   >  2:378476/1‑141 (MQ=255)

                                                                       aaTTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCt                                                  <  2:147591/141‑1 (MQ=255)

                                                                        aTTACAATAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCtt                                                 <  2:134427/141‑1 (MQ=255)

                                                                         ttACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCttt                                                <  2:66452/141‑1 (MQ=255)

                                                                          tACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCtttt                                               <  2:48786/141‑1 (MQ=255)

                                                                                       tAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTataata                                  >  2:378030/1‑141 (MQ=255)

                                                                                        aaaTTATACGGCTGGAAATTCAATGCTGTAAAAATAGAAAAAAAAAAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAatat                                 <  2:424447/141‑1 (MQ=255)

                                                                                             aaactgccagAAATTAAATGCTATAAAAATAGAAAAAAAAAAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAg                            <  2:191280/132‑1 (MQ=255)

                                                                                                 ggCTGGAAATTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCtat                        <  2:464662/141‑1 (MQ=255)

                                                                                                      gAAATTCAAAGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTatat                   <  2:49423/141‑1 (MQ=255)

                                                                                                        aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAGCAATAATTATGAATTTCTTTTTATTTCTATAATATCAAAGTTATTTTATGa                 >  2:477139/1‑141 (MQ=255)

                                                                                                        aaTTCAATGCTGTAAAAATAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATACAAGATATTATATGa                 >  2:76877/1‑141 (MQ=255)

                                                                                                                       aaaTAGACATATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTaa  <  2:259887/141‑1 (MQ=255)

TCATCTAATATTTTATATAATTCATATAAGTGTAGTATTAACGTTTTCTACTTTATCTATAAAATATTTAGAATTACATTAGAATTTTAAATTATACGGCTGGAAATTCAATGCTGTAAAAATAGACAGATTTTAAAAAAGTAGTAATAAAAAGTCTAAGTTTTATCTTTGTAATAAACTTCGACTATATTTAAAAATAAATATGAATGTCTTTTAATTTCTATAATATCAAAGCTATTATATGATTTGAAATTTTGTAA  >  CP000730/58316‑58575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A