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
A1 F169 I1 R1	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,086,905	(A)_8→7	intergenic (‑56/‑629)	USA300HOU_1946 ← / → chp	hypothetical protein/chemotaxis inhibitory protein CHIPS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,086,898	0	A	.	96.9%	137.8 / ‑1.5	32	intergenic (‑49/‑636)	USA300HOU_1946/chp	hypothetical protein/chemotaxis inhibitory protein CHIPS
Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (18/13); total (18/14)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

CTAGCTTGTGCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAA  >  CP000730/2086755‑2087041

cTAGCTTGTGCATCATGTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTaaaaa                                                                                                                                             <  2:47894/148‑1 (MQ=255)

       gtgCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACa                                                                                                                                     >  2:1579/1‑148 (MQ=255)

                  ttATATAGATTAGTTAATAGAGGAGATGCTAAAATGATTGTTAAAGTTCCCGAAAGTATAGATTTTCTAATTTTCATTTTTTATTCAAATTAGTAATTAGTACTAATTTATTTTAA‑AAAAAAAAAAAAAAAAGTACATTAATTATTCa                                                                                                                          <  2:258644/148‑1 (MQ=255)

                          aTTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTCTTCTCCTTAGTAATTAGTACTAATTTCTTTTTATGACTGACT‑TAAAAAAGTACATTAATTATCCATCAACtat                                                                                                                  >  2:164354/1‑148 (MQ=255)

                                 aCTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtc                                                                                                           >  2:30092/1‑148 (MQ=255)

                                    aGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttc                                                                                                        <  1:179561/148‑1 (MQ=255)

                                    aGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAAAtcttc                                                                                                        >  2:133286/1‑148 (MQ=255)

                                    aGTGGNGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGAATTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑NAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttc                                                                                                        <  1:72797/148‑1 (MQ=255)

                                     gtggtgATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttct                                                                                                       >  1:20604/1‑148 (MQ=255)

                                          taTGCTAAAACTATTGCTAAAGTGCCCTCAATTATAGATTTTCTAATTTTCATTTTTTAGTCGCCTTAGGAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  1:331272/147‑1 (MQ=255)

                                          gATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGTAT‑ATAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  1:303871/148‑1 (MQ=255)

                                          gATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  1:166801/148‑1 (MQ=255)

                                                    cGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAAtt                                                                                        <  2:163047/148‑1 (MQ=255)

                                                        tGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATtaata                                                                                    <  2:196097/148‑1 (MQ=255)

                                                         gCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATtaataa                                                                                   >  2:395835/1‑148 (MQ=255)

                                                           tAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTACAGAGCTCCTTGTATGAAATGTAAATTAATAAAt                                                                                 >  2:187512/1‑148 (MQ=255)

                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  1:1579/148‑1 (MQ=255)

                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  1:90470/148‑1 (MQ=255)

                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  1:312170/148‑1 (MQ=255)

                                                                                 tttCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTAtt                                                           <  1:219589/148‑1 (MQ=255)

                                                                                         tttCATTTTTTTTTTTTTTTTGTAATTAGAACAAATTTATTTTAATTACTGACT‑AAAACAAGTAAATAAATTATTCATTAACTATATAGATTTTCTTATTAAATTAAAATTAATAAATTATAAAATTTACATATTTTATTGTAttttt                                                   >  2:84315/1‑146 (MQ=255)

                                                                                                          cTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAgg                                  >  2:127286/1‑148 (MQ=255)

                                                                                                                aaTTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCa                            >  2:79416/1‑148 (MQ=255)

                                                                                                                aaTTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCa                            >  1:361092/1‑148 (MQ=255)

                                                                                                                       aCTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATCGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATATATAGAAAAACAAAAAAAGGTAAGAACCGAAAt                     >  2:135256/1‑148 (MQ=255)

                                                                                                                       aCTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAAt                     >  2:392484/1‑148 (MQ=255)

                                                                                                                        cTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATg                    >  2:250521/1‑148 (MQ=255)

                                                                                                                           atttatttTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCtt                 <  1:337822/148‑1 (MQ=255)

                                                                                                                           atttatttTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCtt                 >  1:185256/1‑148 (MQ=255)

                                                                                                                                  ttAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACt          >  2:137581/1‑148 (MQ=255)

                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      >  2:98366/1‑148 (MQ=255)

                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      <  1:274375/148‑1 (MQ=255)

                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCCTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      >  2:358354/1‑148 (MQ=255)

                                                                                                                                      aagaaggacaaaacaaaATACATTAATTATTCATTAAATATATAAATCTTCTTATTAAATGAAAAATAATAACTTAGAAAATTGATATGCCTTATTTTATTTAAAAAAAAAAAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTcc       <  2:229819/139‑1 (MQ=255)

                                                                                                                                          tgact‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATaa  <  1:30092/148‑1 (MQ=255)

CTAGCTTGTGCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAA  >  CP000730/2086755‑2087041

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