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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,788,238	G→A	pseudogene (1842/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,788,238	0	G	A	100.0%	156.3 / NA	48	pseudogene (1842/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/28); total (20/28)

TTAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGT  >  NC_000913/2788110‑2788367

ttAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAg                                                                                                                         <  2:207113/139‑1 (MQ=255)

 ttgCAATGGGAAATATAGCCGCTCTGCCGGTCAGCAAGGCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAgg                                                                                                                        <  2:329031/137‑1 (MQ=255)

  aGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGt                                                                                                                       >  1:173552/1‑139 (MQ=255)

    cAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTg                                                                                                                     <  2:445127/139‑1 (MQ=255)

      aTGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGct                                                                                                                   <  2:487174/139‑1 (MQ=255)

                 aGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcag                                                                                                        >  2:431316/1‑139 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                  <  2:3137/127‑1 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                  >  1:3137/1‑127 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                      >  2:613404/1‑139 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                      >  1:738827/1‑139 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                      >  2:465914/1‑139 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                      >  2:512564/1‑139 (MQ=255)

                   ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                      >  1:253597/1‑139 (MQ=255)

                      ctctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATTGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGct                                                                                                   <  1:465914/139‑1 (MQ=255)

                      ctctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGct                                                                                                   >  2:199485/1‑139 (MQ=255)

                      ctctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGct                                                                                                   >  1:568037/1‑139 (MQ=255)

                        ctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGctct                                                                                                 >  1:134649/1‑139 (MQ=255)

                              ttCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                  >  2:509149/1‑116 (MQ=255)

                              ttCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                  <  1:509149/116‑1 (MQ=255)

                                     ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                    <  2:255874/139‑1 (MQ=255)

                                      gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                   <  1:199485/139‑1 (MQ=255)

                                      gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                   <  1:123759/139‑1 (MQ=255)

                                      gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                   <  2:253597/139‑1 (MQ=255)

                                      gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                   <  2:495330/139‑1 (MQ=255)

                                         tttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGTGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                                <  2:165667/139‑1 (MQ=255)

                                          ttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCAt                                                                               <  1:530297/139‑1 (MQ=255)

                                               ttACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATtatat                                                                          <  1:288027/139‑1 (MQ=255)

                                                    gggATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                     <  1:613404/139‑1 (MQ=255)

                                                    gggATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                     <  2:223300/139‑1 (MQ=255)

                                                       aTGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATaa                                                                  <  2:568037/139‑1 (MQ=255)

                                                        tGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                    >  1:118759/1‑120 (MQ=255)

                                                        tGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                    <  2:118759/120‑1 (MQ=255)

                                                           ccAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCa                                                              <  2:173552/139‑1 (MQ=255)

                                                                         cAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                          <  2:101614/65‑1 (MQ=255)

                                                                         cAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                          >  1:101614/1‑65 (MQ=255)

                                                                          aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCa                                               >  1:156455/1‑139 (MQ=255)

                                                                             gACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCAttt                                            <  1:155466/139‑1 (MQ=255)

                                                                               cTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGa                                          <  2:738827/139‑1 (MQ=255)

                                                                                                      tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                     >  2:493644/1‑57 (MQ=255)

                                                                                                      tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                     <  1:493644/57‑1 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAg                                                                <  1:698352/84‑1 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAg                                                                >  2:698352/1‑84 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAgc                                                  <  2:771206/98‑1 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAgc                                                  >  1:771206/1‑98 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCtt         <  1:512564/139‑1 (MQ=255)

                                                                                                                tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCtt         >  1:664311/1‑139 (MQ=255)

                                                                                                                    cggTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGt     <  2:156455/139‑1 (MQ=255)

                                                                                                                       tGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGt  >  1:475541/1‑139 (MQ=255)

TTAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGT  >  NC_000913/2788110‑2788367

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A