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	1,063,912	+C	coding (577/1218 nt)	ywtF ←	Putative transcriptional regulator YwtF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,063,909	1	.	C	88.9%	151.4 / 14.2	45	coding (580/1218 nt)	ywtF	Putative transcriptional regulator YwtF
Reads supporting (aligned to +/- strand): ref base . (3/2); new base C (24/16); total (27/18)
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

TATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAG  >  USA300TCH1516_ALE/1063762‑1064049

tATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑a                                                                                                                                               <  3:156008/148‑1 (MQ=255)

tATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑a                                                                                                                                               <  3:110544/148‑1 (MQ=255)

        ttATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑c                                                                                                                                             <  2:5951/141‑1 (MQ=255)

        ttATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCctttt                                                                                                                                      >  4:302746/1‑148 (MQ=255)

            cAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTttttaa                                                                                                                                   >  3:223156/1‑148 (MQ=255)

              aTAGAATCAACTTCCTTTGCTTTTTGGACTACACTCTTTATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCcttt                                                                                                                                       <  2:37482/141‑1 (MQ=255)

              aTAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTttttaatt                                                                                                                                 <  4:127648/148‑1 (MQ=255)

                        cTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTttttaatttta                                                                                                                              >  1:35557/1‑141 (MQ=255)

                           ccTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAg                                                                                                                    >  4:127270/1‑148 (MQ=255)

                                    tttGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtg                                                                                                           <  3:201248/148‑1 (MQ=255)

                                     ttGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtgt                                                                                                          <  4:132675/148‑1 (MQ=255)

                                      tGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCtgtg                                                                                                         >  3:409488/1‑148 (MQ=255)

                                       ggAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTgtgt                                                                                                        >  3:131994/1‑148 (MQ=255)

                                        gattAAAATCTTAATTAATTCCACTTGACGTTGTCCACGTTTTACGTCTGAATCATCATGTCTAGATCTGGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGGAA‑A‑CCCTTTTTTAATATTAATCTTACAAGTATAATCTGTGtt                                                                                                       >  4:289570/4‑148 (MQ=255)

                                               aTCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCa                                                                                                <  4:183122/148‑1 (MQ=255)

                                                  ttaattaaTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCAttt                                                                                             <  3:116496/148‑1 (MQ=255)

                                                  ttaattaaTTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCAttt                                                                                             <  3:116602/148‑1 (MQ=255)

                                                            ccATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATg                                                                                   <  4:232744/148‑1 (MQ=255)

                                                            ccATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATg                                                                                   >  3:25478/1‑148 (MQ=255)

                                                             cATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGt                                                                                         <  2:35557/141‑1 (MQ=255)

                                                             cATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATgg                                                                                  >  4:118306/1‑148 (MQ=255)

                                                               tttGACGTTGTCCACGTTTTACGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTACAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTCAGTCGTATGGca                                                                                >  4:95298/1‑148 (MQ=255)

                                                                 tgtcGTTGTCCACGTTTTAAGTCTGAATCATCGTGTTTAGTTCTAGGCTCTGCTAATGCCTCATCACCATTTAA‑TTTTTGG‑TCC‑CCCTTTTTTCATTTTGTTCTTTCCAGTATCTTCTGTGTTAGGTTCATTTAAGTCGTATGGcaca                                                                              <  4:97062/145‑1 (MQ=255)

                                                                 tGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGcaca                                                                              <  4:50517/148‑1 (MQ=255)

                                                                     gTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCAcatcat                                                                          <  3:172202/148‑1 (MQ=255)

                                                                           cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTATTTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  4:71315/1‑148 (MQ=255)

                                                                           cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTATTTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATAATAGtata                                                                    >  4:231933/1‑148 (MQ=255)

                                                                           cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTTATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  4:231940/1‑148 (MQ=255)

                                                                           cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGtata                                                                    >  3:222787/1‑148 (MQ=255)

                                                                           cACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTCTAGTTAAGTCGTATGGCAcatca                                                                           >  2:48058/1‑141 (MQ=255)

                                                                                  tAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCACAGTATCTGccccc                                                             >  4:245597/1‑148 (MQ=255)

                                                                                        tGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAATTTTTTTT‑T‑T‑TTTTTTTTTAATTTTAATCTTACCAGTATTTTCTGTGTTAGGTTCATTTAAGTCGTATGGCACTTCCTAGTATATGCCACCAAGCTc                                                       >  4:55644/1‑148 (MQ=255)

                                                                                        tGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTc                                                       >  3:45004/1‑148 (MQ=255)

                                                                                        tGAATCATGAAGCCTAGTACTAGCAACTGCTAAAGCCTCATCACCATCTAA‑TTTTTGG‑T‑ACCCCTTTTATAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTc                                                       >  4:55653/1‑148 (MQ=255)

                                                                                         gAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCa                                                      <  4:92147/148‑1 (MQ=255)

                                                                                                  tgTCTAGTTCTAGCAACTGCTAAGGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTGTCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCAtt                                                    <  1:48058/141‑1 (MQ=255)

                                                                                                        gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTTTTACTAGTATCATCTGTGTTATGTTCATTTAAGTCGTATGGCACATCATTGTCTTTGTCTCCAAGCTTATTTTCAGTCTCTACa                                       >  4:101268/1‑148 (MQ=255)

                                                                                                        gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCTTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                       >  4:187504/1‑148 (MQ=255)

                                                                                                        gTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                       >  4:227306/1‑148 (MQ=255)

                                                                                                              gCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCt                                 >  3:388398/1‑148 (MQ=255)

                                                                                                               cAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACa                                       >  2:25058/1‑141 (MQ=255)

                                                                                                                         aGCCTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGAc                      <  3:66340/148‑1 (MQ=255)

                                                                                                                           ccTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGActc                    >  3:258540/1‑148 (MQ=255)

                                                                                                                           ccTCATCACCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCACTTACAGCCTCGACAAATGCTTTCATATTGActc                    >  3:158074/1‑148 (MQ=255)

                                                                                                                              catcaCCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTTTTTTTTTTCTTACCAGTATCATCTGTGTTAGTTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTTACTCTca                 >  4:45322/1‑148 (MQ=255)

                                                                                                                              catcaCCATTTAA‑TTTTTGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTca                 <  4:367639/148‑1 (MQ=255)

                                                                                                                                            tttttGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAAc    <  3:118302/148‑1 (MQ=255)

                                                                                                                                              tttGG‑T‑ACCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAg  <  3:381075/148‑1 (MQ=255)

TATCAAGTTTATCAATAGAATCAACTTCCTGTGCTTTTTGGAATAAAATCTTAATTAATTCCATTTGACGTTGTCCACGTTTTAAGTCTGAATCATGATGTCTAGTTCTAGCAACTGCTAAAGCCTCATCACCATTTAA‑TTTTTGG‑T‑A‑CCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAG  >  USA300TCH1516_ALE/1063762‑1064049

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