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	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,613,762	T→C	intergenic (‑31/‑37)	scpA ← / → USA300HOU_RS08000	Segregation and condensation protein A/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,613,762	0	T	C	97.1%	117.4 / NA	34	intergenic (‑31/‑37)	scpA/USA300HOU_RS08000	Segregation and condensation protein A/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (19/14); total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAT  >  USA300TCH1516_ALE/1613637‑1613897

tCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAtt                                                                                                                   >  3:49225/1‑148 (MQ=255)

tCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAAtt                                                                                                                   >  3:283981/1‑148 (MQ=255)

  aaaTTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTgg                                                                                                                 >  3:292643/1‑148 (MQ=255)

   aaTTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTa                                                                                                                       >  2:28902/1‑141 (MQ=255)

           gATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAAc                                                                                                        <  3:238875/148‑1 (MQ=255)

             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:363535/1‑148 (MQ=255)

             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:251894/1‑148 (MQ=255)

             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  4:114724/1‑148 (MQ=255)

             tAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaa                                                                                                      >  3:355315/1‑148 (MQ=255)

               aGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACaaaa                                                                                                    <  3:121959/148‑1 (MQ=255)

                  tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc                                                                                                 >  4:47320/1‑148 (MQ=255)

                  tGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGc                                                                                                 >  4:308667/1‑148 (MQ=255)

                        aaTAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAgg                                                                                           >  3:118909/1‑148 (MQ=255)

                               cTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGAt                                                                                    >  4:81600/1‑148 (MQ=255)

                                   tGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAAt                                                                                >  3:45385/1‑148 (MQ=255)

                                      tCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTc                                                                             <  3:139678/148‑1 (MQ=255)

                                       ccATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCt                                                                            <  3:309300/148‑1 (MQ=255)

                                         aTTGAGAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:269435/148‑1 (MQ=255)

                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  3:304388/148‑1 (MQ=255)

                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:61846/148‑1 (MQ=255)

                                         aTTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  4:264284/148‑1 (MQ=255)

                                          ttGAAAGCATTTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAAt                                                                                <  2:16456/141‑1 (MQ=255)

                                             aaaGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTAAAGCACGAAAATAACTTACTTTTAAAATAAAAAAAAAAAAAAATGCAACAGGCACTGATAAATTTCtattata                                                                      <  4:347368/148‑2 (MQ=255)

                                                gCATCTAATTTAACTTCATACCTAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCtat                                                                          <  1:12458/141‑1 (MQ=255)

                                                             cTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCa                                                      >  4:213215/1‑148 (MQ=255)

                                                                               ccTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCa                                    <  4:52880/148‑1 (MQ=255)

                                                                                 tCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg                                  >  3:203514/1‑148 (MQ=255)

                                                                                        gCGTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATg                                  <  1:28902/141‑1 (MQ=255)

                                                                                          gTCATATGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTag                         >  4:33494/1‑148 (MQ=255)

                                                                                             atatGTGCATAATTCTCTAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTagaag                      >  3:287180/1‑148 (MQ=255)

                                                                                                           ctctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCt        >  3:219658/1‑148 (MQ=255)

                                                                                                           ctctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCt        >  3:234427/1‑148 (MQ=255)

                                                                                                             ctAAAATATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGa             >  1:18725/1‑141 (MQ=255)

                                                                                                                 aaTATTATAGCACGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAt  <  3:378681/148‑1 (MQ=255)

TCAAATTTTTGGATAAGATGCAGCAATAAATCTAATGGTCCATTGAAAGCATCTAATTTAACTTCATACATAATATCTACCTCGTATTGCGTCATATGTGCATAATTCTCTAAAATATTATAGCATGAAAATAACTTACTTTTAAATTGGGGTGATAACAAAATGCAACAGGCACTGATAAATTTCTATTATCAATTTCATACTAAGCAACATTATTTCCTATGTCATGACATTTTAGAAGATGCATGGAAAGCTGAAAAT  >  USA300TCH1516_ALE/1613637‑1613897

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

GATK/CNVnator alignment

N/A