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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	942,060	C→G	46.4%	intergenic (‑31/+218)	USA300HOU_0905 ← / ← mnhG2	hypothetical protein/CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit G

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	942,060	0	C	G	46.4%	7.3 / 28.8	29	intergenic (‑31/+218)	USA300HOU_0905/mnhG2	hypothetical protein/CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit G
Reads supporting (aligned to +/- strand): ref base C (7/8); new base G (7/6); total (14/15)
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

TCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAG  >  CP000730/941923‑942193

tCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGtt                                                                                                                                    >  1:22124/1‑141 (MQ=255)

  gtgtGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGttgc                                                                                                                                  >  1:2001/1‑139 (MQ=255)

  gtgtGGGTCAAGGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTAc                                                                                                                                  <  1:110295/141‑1 (MQ=255)

   tgtgGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACg                                                                                                                                 >  2:277037/1‑141 (MQ=255)

       ggTCAATGATTGTTAATCGGTCTGTTGTTACTCCGCTTGATAATAGTTTTTGTG‑CGATTGCCGTTCCCTGTATGCAACCGACGATAAGTTTCCAATGCATAATAAACCCTCTCTCTTTTTAAAACGTAATGGTCACGAttc                                                                                                                             >  2:99632/1‑140 (MQ=255)

       ggTCAATGATAGTTAAACGGACAGTTGTTACTCCGCTTGATAATAGTTTTTGTG‑CGTTTGCATTTTACTGTATACCATCGCCGATAAATGTCAAATGCATAGTAAAACGTTTCTCTTTTTGAATCGTGATGGttgatagta                                                                                                                             >  2:99653/1‑134 (MQ=255)

              gATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAattt                                                                                                                      >  1:80558/1‑140 (MQ=255)

               aTTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAattat                                                                                                                     <  1:7886/141‑1 (MQ=255)

                  gTTAATAGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATGGCAGTTACCTGTATGCGAACGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAattattat                                                                                                                  >  2:52153/1‑141 (MQ=255)

                   ttAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAattattatt                                                                                                                 <  1:3327/141‑1 (MQ=255)

                      aTCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAGACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATc                                                                                                              <  1:121646/141‑1 (MQ=255)

                                      tCCGCTTGATAATAGCTTTAGTC‑AGTTTGGAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAacaaca                                                                                              >  2:60368/1‑141 (MQ=255)

                                       ccGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACAt                                                                                             >  2:109799/1‑141 (MQ=255)

                                              ataataGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGc                                                                                      >  1:209716/1‑141 (MQ=255)

                                                 ataGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCaat                                                                                   <  1:271196/141‑1 (MQ=255)

                                                  acagttttGTGTCGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATTAACCCTCTCTCTTTTTACAACGTAATGGTTACGATTTATAATTATTATTATCATACTACATAACGACATGAAAGGCaat                                                                                   <  2:81808/137‑1 (MQ=255)

                                                                 ttGCAGTACCCTGTATGCCACCGCCGATAATTGTCCAATTCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGata                                                                    <  1:261119/141‑1 (MQ=255)

                                                                     aGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACTATTTATAATTATTATTATCATAATACATAAGGACATGAAAGCCAATTAAATGAAAGTGAAATATg                                                                >  2:41122/1‑141 (MQ=255)

                                                                             gTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAgg                                                        >  2:221537/1‑141 (MQ=255)

                                                                             gTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGATACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAgg                                                        <  2:36481/141‑1 (MQ=255)

                                                                               aTGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGc                                                      >  2:273225/1‑141 (MQ=255)

                                                                                             aaTTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCaa                                        <  1:197518/141‑1 (MQ=255)

                                                                                                 gcccAAAGAATAATAAAACCTCTCACTCTATAAAACGTAATCGTTAAGCTTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGaa                                    <  2:249275/139‑1 (MQ=255)

                                                                                                            aataaAACCCCTCTCTTTTTCAAACGTAATCTTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGa                         <  1:214239/141‑1 (MQ=255)

                                                                                                                aaaCCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGaaaaa                     <  1:277037/141‑1 (MQ=255)

                                                                                                                        ctctTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTGGTCAAAGAAAAAATCATTGAAAAAGAGGAAAc             >  2:53279/1‑141 (MQ=255)

                                                                                                                           ttttcAAAACCTATTTGTTACGTTTGATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAAt          <  2:281029/141‑1 (MQ=255)

                                                                                                                              ttAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTc       <  1:184960/141‑1 (MQ=255)

                                                                                                                                  aaCGTAATGGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAG‑AAAAATCATTGAAAAAGAGGTAACAATGTCAAAAg  <  1:153659/141‑1 (MQ=255)

TCGTGTGGGTCAATGATTGTTAATCGGTCTGTTGTTAATCCGCTTGATAATAGTTTTTGTG‑CGATTGCAGTTCCCTGTATGCCACCGCCGATAATTGTCCAATGCATAATAAAACCTCTCTCTTTTTAAAACGTAATCGTTACGATTTATAATTATTATTATCATAATACATAACGACATGAAAGGCAATTAAATTAAAGAGATATATGTAGATAGGGCGAATCTGTAGTCAAAGAAAAAATCATTGAAAAAGAGGTAACAATGTCAAAAG  >  CP000730/941923‑942193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A