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 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	933,033	T→C	100%	intergenic (‑74/‑27)	nfuA ← / → USA300HOU_RS04645	Fe/S biogenesis protein NfuA/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	933,033	0	T	C	97.4%	121.1 / ‑4.0	38	intergenic (‑74/‑27)	nfuA/USA300HOU_RS04645	Fe/S biogenesis protein NfuA/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/18); total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAAGACGTTCAATAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAATCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTACAGCCGCTATTAA  >  USA300TCH1516_ALE/932901‑933165

cGAAGACGTTCAATAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGAAAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCaa                                                                                                                               >  1:152170/1‑140 (MQ=255)

 gAAGACGTTCAATAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCaaa                                                                                                                              <  2:30217/140‑1 (MQ=255)

    gACGTTCAATAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCa                                                                                                                           <  2:281368/140‑1 (MQ=255)

             tAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGAt                                                                                                                  <  1:154468/140‑1 (MQ=255)

                     ggtACTTGTTCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGGGATGAATTTGATAATCTTTTTGAGTATATTATAAGAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAatatat                                                                                                          <  2:124279/138‑1 (MQ=255)

                     gCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGCGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAatatat                                                                                                          >  2:216955/1‑140 (MQ=255)

                      cTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTAGATAATCTTTATTAGTATATTATAATAGATAGTGAAATAAAAACATATCAAACCAATGGTGTATAAAAATATg                                                                                                         >  1:262985/1‑140 (MQ=255)

                               cAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTg                                                                                                <  1:5021/140‑1 (MQ=255)

                                   cATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAgtg                                                                                            <  1:359850/140‑1 (MQ=255)

                                               ttCAGTAGGCATCAGGCATGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATg                                                                                <  2:401086/140‑1 (MQ=255)

                                                tCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCTATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATgg                                                                               <  2:293891/140‑1 (MQ=255)

                                                   gTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAATCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGc                                                                            <  2:346163/140‑1 (MQ=255)

                                                         aTCAGGCAAGGCTCCTTTCGGGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAGATATATGGAGCTTGTGAGTGTGGTAGTTTATGGGGCAGATGt                                                                      <  2:364157/140‑1 (MQ=255)

                                                          tCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTCTCGAATAAATAGGGGATAAATATATAGAACACGTAAGAGTGATAGTTAATGAGGAAGATGtt                                                                     >  1:126672/1‑140 (MQ=255)

                                                            aGGCACGTCTCCTTCCGAGAGATGAACTTGATAATCCTTATTAGTATATTATAATAGATAGTGTAATAACATCCTATCAAACCAACGTGGGTTAAATATATGGAGCACGAGAGTGCAGTCGTTTAAGGAGGAGATGTtat                                                                   >  2:125124/1‑140 (MQ=255)

                                                            aGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTtat                                                                   >  1:348804/1‑140 (MQ=255)

                                                            aGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTtat                                                                   >  2:85875/1‑140 (MQ=255)

                                                            aGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATAGGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTtat                                                                   >  2:344200/1‑140 (MQ=255)

                                                                           tggaagaTGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGt                                                    <  1:547052/136‑1 (MQ=255)

                                                                              gagaTGAATTTGTTAAGTTTTATTAGTATAGTATAAGAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAAGATATGGATCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTaa                                                 <  2:152170/140‑1 (MQ=255)

                                                                                 aTGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATgc                                              >  2:350029/1‑140 (MQ=255)

                                                                                   gAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATgcgc                                            >  1:94659/1‑140 (MQ=255)

                                                                                          aTAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATc                                     <  2:392303/140‑1 (MQ=255)

                                                                                            aaTCTTTATTAGTATATTATAATAGATAGTGTACTAAAAACCTATTAAACCAATGGGGGATAAATATATGGGGCACGTGAGTGTGGTAGTTTATGGGGCAGAGGTTATAAAAAGATATTTTGTTTATGCGCCAACATCGa                                   <  1:267412/140‑1 (MQ=255)

                                                                                             aTCTTTATTAGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGAGTGGTAGTTTAAGGGACAGAAGATATATGTACAAGTTGCATTAATACGCCAACATCGaa                                  >  1:130567/1‑140 (MQ=255)

                                                                                                  tattaGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGata                             >  2:437248/1‑140 (MQ=255)

                                                                                                    ttaGTATATTATAATAGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATGtt                           >  2:245152/1‑140 (MQ=255)

                                                                                                             tataATAGATAGTGTAATAAACACCTAACAAACCAATGGGGGATAAATATATGGAGCACGTGAGAGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACggg                  >  2:528732/1‑140 (MQ=255)

                                                                                                              ataataGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGc                 <  1:363122/140‑1 (MQ=255)

                                                                                                                aataGATAGTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGAAACATGCGTGAATGCGCCAACATCGAAAGATATTTATGACTGGCTa               >  1:512072/1‑140 (MQ=255)

                                                                                                                 atagatagTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTAc              >  2:185743/1‑140 (MQ=255)

                                                                                                                 atagatagTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGGGCGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTAc              >  1:118599/1‑140 (MQ=255)

                                                                                                                    gatagTGTAATAAAGACCTGTCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTACAGc           >  1:358828/1‑140 (MQ=255)

                                                                                                                      tagTGTAATAAAAACCTAGCAAACTAATGGGGGATAAATAGAGAGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATTTGCAACTTGCGTTAATTCGCCAACATCGAAATATATTTATGACTGGCTACAGCCg         <  2:48471/140‑1 (MQ=255)

                                                                                                                       agTGTAATAAAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTACAGCCGc        <  1:216955/140‑1 (MQ=255)

                                                                                                                           taataaAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGGCAACATCGAAAGATATTTATGACTGGCTACAGCCGCTAtt    <  1:429362/140‑1 (MQ=255)

                                                                                                                           taataaAAACCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTACAGCCGCTAtt    <  1:429346/140‑1 (MQ=255)

                                                                                                                             ataaAAACCTATCAAACCAATGGGGGATAAATAAAAGGAGCACGTGAATGTAGTAGTTGATGGGGCAGATGTTATATGTGCATGTTGCGTTAATGCGCCAACATCGAAAGAGATTTATAACTGGCTAGAGCCGCTATTaa  >  2:362163/1‑140 (MQ=255)

CGAAGACGTTCAATAACTTCTGCTACTTGATCAAACATCGTTGTATCTTCAGTAGGCATCAGGCAAGTCTCCTTTCGAGAGATGAATTTGATAATCTTTATTAGTATATTATAATAGATAGTGTAATAAAAATCTATCAAACCAATGGGGGATAAATATATGGAGCACGTGAGTGTGGTAGTTTATGGGGCAGATGTTATATGTGCAAGTTGCGTTAATGCGCCAACATCGAAAGATATTTATGACTGGCTACAGCCGCTATTAA  >  USA300TCH1516_ALE/932901‑933165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A