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
A17 F172 I1 R2	29	34.5	745914	96.0%	716077	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	469,786	A→G	G118G (GGA→GGG)	USA300HOU_0445 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	469,786	0	A	G	93.1%	87.2 / ‑1.0	29	G118G (GGA→GGG)	USA300HOU_0445	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/2); new base G (17/10); total (17/12)
Fisher's exact test for biased strand distribution p-value = 1.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.61e-01

CGAGATGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAAAACT  >  CP000730/469649‑469922

cGAGATGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCat                                                                                                                                       >  2:128172/1‑141 (MQ=255)

  agaTGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACatta                                                                                                                                     <  2:332025/141‑1 (MQ=255)

       gCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTg                                                                                                                                >  1:282799/1‑141 (MQ=255)

            tttAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAg                                                                                                                           <  1:79418/141‑1 (MQ=255)

             ttAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGa                                                                                                                          <  2:44011/141‑1 (MQ=255)

                aaaaGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACAt                                                                                                                       >  2:134887/1‑141 (MQ=255)

                              gggATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGc                                                                                                         >  2:273482/1‑141 (MQ=255)

                                    tgGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTc                                                                                                   >  1:181312/1‑141 (MQ=255)

                                         gATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGa                                                                                              <  2:323103/141‑1 (MQ=255)

                                         gATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATACCCAGa                                                                                              <  2:115855/141‑1 (MQ=255)

                                                     tttCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATta                                                                                  >  2:271138/1‑141 (MQ=255)

                                                      ttCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATtat                                                                                 <  2:169660/141‑1 (MQ=255)

                                                        cGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATaa                                                                               <  1:147475/141‑1 (MQ=255)

                                                           cAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGt                                                                            <  1:321355/141‑1 (MQ=255)

                                                                    taaACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACTGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTtgaaatgaa                                                                   >  2:127160/1‑141 (MQ=255)

                                                                        cAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAGTAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGaaaaaa                                                               >  2:236488/1‑140 (MQ=255)

                                                                           cgtcgattgattAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAaataat                                                            <  2:292855/137‑1 (MQ=255)

                                                                              ggATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATaaa                                                         >  1:241370/1‑141 (MQ=255)

                                                                               gATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATaaaa                                                        <  1:10208/141‑1 (MQ=255)

                                                                                     gTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCt                                                  >  1:13718/1‑141 (MQ=255)

                                                                                       aaTGAAGGTATGGGCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCtta                                                <  2:45402/141‑1 (MQ=255)

                                                                                        aTGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCttat                                               >  1:357908/1‑141 (MQ=255)

                                                                                               tATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATaa                                        >  1:328892/1‑141 (MQ=255)

                                                                                                 tGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAg                                      >  2:307366/1‑141 (MQ=255)

                                                                                                                atagaAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATc                       <  1:322272/141‑1 (MQ=255)

                                                                                                                           cGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAgaga            >  1:114477/1‑141 (MQ=255)

                                                                                                                               cTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAg        >  1:19055/1‑141 (MQ=255)

                                                                                                                                    aaGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAAAAc   >  2:261907/1‑141 (MQ=255)

                                                                                                                                     aGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAAAACt  >  2:173257/1‑141 (MQ=255)

CGAGATGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAAAACT  >  CP000730/469649‑469922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A