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 F52 I1 R1	27	78.9	1851050	96.3%	1782561	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	607,884	G→A	R209* (CGA→TGA)	dck ←	Deoxyadenosine/deoxycytidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	607,884	0	G	A	98.2%	171.7 / NA	55	R209* (CGA→TGA)	dck	Deoxyadenosine/deoxycytidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (34/20); minor base C (0/1); total (34/21)
Fisher's exact test for biased strand distribution p-value = 3.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTT  >  USA300TCH1516_ALE/607747‑608015

tataTGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTAATTGATTGTATTTTTGAATAATTCAAGc                                                                                                                                  <  2:198802/141‑1 (MQ=255)

    tgtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                              <  2:591954/141‑1 (MQ=255)

     gtgAATTAATGTATTCGATAGTATTGATAATATATTCGTTAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAGTAATTCAAGCAAttt                                                                                                                             <  1:684503/141‑1 (MQ=255)

             aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTCCTTGTCGATATGTTTGTATAATTCAAGCATTTTTGTTTATc                                                                                                                     >  1:602753/1‑141 (MQ=255)

             aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  2:531517/1‑141 (MQ=255)

             aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  1:753119/1‑141 (MQ=255)

             aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     <  1:765251/141‑1 (MQ=255)

             aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  2:11163/1‑141 (MQ=255)

              tGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCa                                                                                                                    <  2:550705/141‑1 (MQ=255)

               gTATTCGATAGAATTGATAAAATAATAGATAGTATTTGTCGATTATACAGAGAATATACACATATACGTTATGTCTGTGGCTTTCTATCGTGTATCGATCTACCTAAATGTTTGAATAATTCAAGCAAttttttttgacat                                                                                                                   >  2:286349/1‑136 (MQ=255)

                     gATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAtt                                                                                                             >  1:771511/1‑141 (MQ=255)

                      aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            >  1:713761/1‑141 (MQ=255)

                      aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            <  1:820857/141‑1 (MQ=255)

                      aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            >  1:5540/1‑141 (MQ=255)

                            ttGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCACTTTTGTTTATCATAGGATTTAAAGAt                                                                                                      >  1:262489/1‑141 (MQ=255)

                              gATAAAATACTCCATACTCTCAACGGAATATAAATTGAATATAAACAAATACGCTACGTCTTTATTCTTTTATCGTGTATCTACTGGTCGATATGTTTGAATAATTCAAGCATTTTTGTTTATCATAGGATTTAAAGATTc                                                                                                    >  2:407772/1‑141 (MQ=255)

                              gATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGATATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTc                                                                                                    >  1:315843/1‑141 (MQ=255)

                                 aaaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCggg                                                                                                 <  2:51045/141‑1 (MQ=255)

                                  aaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGCAAATTTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:170112/1‑141 (MQ=255)

                                  aaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:720282/1‑141 (MQ=255)

                                  aaaTAATCGATAATAACTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:679551/1‑141 (MQ=255)

                                       atCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCtt                                                                                           <  2:111484/141‑1 (MQ=255)

                                         cGATAATATCTATGGAATATACATTGAATATAAACATATACGCCATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTAt                                                                                         <  1:342431/141‑1 (MQ=255)

                                               tatCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGatat                                                                                   <  2:715485/141‑1 (MQ=255)

                                                 tCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCa                                                                                 >  1:764871/1‑141 (MQ=255)

                                                           ataCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTaa                                                                       >  2:387503/1‑141 (MQ=255)

                                                              cATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAatat                                                                    >  1:11597/1‑141 (MQ=255)

                                                                     tataAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                             <  2:168690/141‑1 (MQ=255)

                                                                      ataAACATATACGGTATGTCTTTAGTGTTTTATCGTGTATCTACTTGTCGATCTGTTTGAATAATTCAAGCAATTTTGTTTATTATAGGATTTAAAGATTGAGGGTCCTTATGGATATCATCTTCATTAATATTGATCCGt                                                            >  2:207651/1‑141 (MQ=255)

                                                                        aaaCATATACTCTAGGTGTTTAGGCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCATTATGGATATCACATTCATTAATATTGATACGTAc                                                          <  1:182113/141‑1 (MQ=255)

                                                                             aataCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTg                                                     <  2:907429/140‑1 (MQ=255)

                                                                              ttaCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTgg                                                    <  2:304147/140‑1 (MQ=255)

                                                                              atactgtATTTCTTGAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCCAGCAATTTTGTTTATCATAGGATTTAACGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTgg                                                    <  2:751826/135‑1 (MQ=255)

                                                                                    tATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTACTATTGATACGTACAACTGGACATGc                                              >  1:290334/1‑141 (MQ=255)

                                                                                          tttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAACTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTCATATTGATACGTACAACTGGACATGCATTaaa                                        >  1:618197/1‑141 (MQ=255)

                                                                                           ttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                       >  1:748719/1‑141 (MQ=255)

                                                                                                cTTTTATCGTGTATCTACTTGTCGGTGTGGTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTAtt                                  >  1:482022/1‑141 (MQ=255)

                                                                                                cTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTAtt                                  >  1:579338/1‑141 (MQ=255)

                                                                                                     aTCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGAGACCTTATGGATATCATATTCATTAATATTGATACGTCCAACTGGACATGCATTAAAGCTATTAATcc                             >  1:174731/1‑141 (MQ=255)

                                                                                                       cGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCaa                           <  2:450228/141‑1 (MQ=255)

                                                                                                        gtgtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAAt                          >  2:39448/1‑141 (MQ=255)

                                                                                                          gtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCg                        >  1:725512/1‑141 (MQ=255)

                                                                                                           tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATCTTGATACGGACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  1:633227/141‑1 (MQ=255)

                                                                                                           tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  2:923177/141‑1 (MQ=255)

                                                                                                           tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  2:155543/141‑1 (MQ=255)

                                                                                                                 cTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGc                 <  1:530239/141‑1 (MQ=255)

                                                                                                                 attGTCGATATGTTTGAATAATTCAAGCAATTTTGATTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATCTCATATTCATTAATATTGATACCTACAGCAGGACATGAATTAAACGAATTAATCCCATCGACATaac                 >  2:801331/2‑139 (MQ=255)

                                                                                                                        atatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTaaa          >  2:915236/1‑141 (MQ=255)

                                                                                                                        atatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTaaa          >  1:710743/1‑141 (MQ=255)

                                                                                                                         tatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAAt         >  1:643018/1‑141 (MQ=255)

                                                                                                                          atGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATa        <  1:85777/141‑1 (MQ=255)

                                                                                                                             tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTCTTAATCCAATCGTCATAGCGATTAAATAGCt     >  2:627171/1‑141 (MQ=255)

                                                                                                                             tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCt     >  1:890916/1‑141 (MQ=255)

                                                                                                                             tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAACCGTCACAGCGTTTaaaacgct     >  2:802971/1‑136 (MQ=255)

                                                                                                                                gAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGACATAGCGTTTAAATAGCtttt  >  2:143157/1‑141 (MQ=255)

TATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTT  >  USA300TCH1516_ALE/607747‑608015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A