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
A17 F109 I0 R1	32	27.2	584098	96.5%	563654	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,360,799	A→G	100%	G66G (GGT→GGC)	adk ←	adenylate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,360,799	0	A	G	97.3%	79.6 / ‑6.2	29	G66G (GGT→GGC)	adk	adenylate kinase
Reads supporting (aligned to +/- strand): ref base A (1/0); major base G (16/10); minor base T (2/0); total (19/10)
Fisher's exact test for biased strand distribution p-value = 5.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATGACAGCATCAATGTTTCTGTCAAGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATACCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTGGGAATTTC  >  CP000730/2360664‑2360931

gatgaCAGCATCAATGTTTCTGTCAAGCTCAGAAATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGGTGCCTa                                                                                                                                  >  2:152335/1‑140 (MQ=255)

          tCAATGTTTCTGTCAAGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTATTGAATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTtc                                                                                                                        >  1:80525/1‑140 (MQ=255)

                tttCTGTCAAGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAgg                                                                                                                  <  1:167143/140‑1 (MQ=255)

                 ttttGTCAAGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGa                                                                                                                 <  1:162804/137‑1 (MQ=255)

                       aaaGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAAt                                                                                                           <  1:278504/139‑1 (MQ=255)

                         aGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTc                                                                                                         <  1:186953/140‑1 (MQ=255)

                             gaGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGGAATTCTTTCCTTCACGATGCCTACCGTCACTTCATCCGGACCTAATTCACCa                                                                                                     >  2:170178/2‑140 (MQ=255)

                                       attattTAATTCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCatat                                                                                           <  2:87487/140‑1 (MQ=255)

                                               aTGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTTTTTTTTTTTCAGAAATTATTTCCTTAACGATTTCGGCAATCGTTTCATCAGGTACTAATTTGGCACGGTCCATTTaatttttt                                                                                   >  2:134805/1‑134 (MQ=255)

                                                tGCCTCAGCTTGCTCGATTGTGCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAg                                                                                  >  1:149494/1‑140 (MQ=255)

                                                        cTTGCTCGATTGTTCTTGGGAGGCCAACTAATAAAAAGCCTTTTTTTGCATCGTCTTCATAAATTCTTTCCTTAAGGATACCTCCAGTCACTTCATCAGGAACTAATTCGCCAAGGCCCATATAAGACGTAGCTTCTTTa                                                                          >  2:170291/1‑140 (MQ=255)

                                                           gCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCt                                                                       >  1:111494/1‑140 (MQ=255)

                                                            cTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTa                                                                      <  1:234585/140‑1 (MQ=255)

                                                                      cTTGAGAAGCCATCTAATAAAAAGCCTTTTTTTGCATAGTCTTAAGAAATTCTTTCCTTAACGATTCCTACAGTCACTTCATCAGGAACTCATTCGTCGCGGGACATATAAGACTTAACTTCTTAACATAATTCAGTttc                                                            >  2:11876/1‑140 (MQ=255)

                                                                                cgtCTAATAAAAAGCCTATTTTTTCATCGTCTTCAGAAAGTCTTTCCTGAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTtata                                                  >  2:26561/3‑140 (MQ=255)

                                                                                  tCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGc                                                <  2:80525/140‑1 (MQ=255)

                                                                                  tCTAATAAAAAGCCTTTTTTTGCATAGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTAACTTCATCAGGAACTAATTCGACACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGc                                                >  2:98819/1‑140 (MQ=255)

                                                                                                    ttttttttttCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCAcc                              >  2:251537/10‑140 (MQ=255)

                                                                                                         aTCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATTTCCCCAGTTg                         >  1:143570/1‑140 (MQ=255)

                                                                                                         aTCGTCTTCAGAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGAATTAGCTTATTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTTTGAACATGACACCAtttt                         >  1:232193/1‑139 (MQ=255)

                                                                                                                   gAAATTCTTTTCTTAACGATGCCTACATTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTgggg               <  1:121117/140‑1 (MQ=255)

                                                                                                                   gAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCCCGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTAAACATGTCACCAGTTGAACTGTtggg               >  1:56075/1‑140 (MQ=255)

                                                                                                                   gAAATTCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGGACATGTCACCAGTTGAAATGTgggg               >  2:282783/1‑140 (MQ=255)

                                                                                                                   gAAATTCGTTCCTTAACGATGCCTACAGTCACTTTAGCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTgggg               <  1:257674/140‑1 (MQ=255)

                                                                                                                        tCTTTCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTg          <  2:42184/140‑1 (MQ=255)

                                                                                                                         cTTTCCTTAACGATGACTTCATTTTGTTCATCAGGAACTAATTCGCCACGGGCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTgg         >  2:206708/1‑140 (MQ=255)

                                                                                                                          tttCCTTAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTggg        >  2:36974/1‑140 (MQ=255)

                                                                                                                                tAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATTTCACCAGTTGAAATTTGGGGTATTGGGAATTTc  >  2:216763/1‑140 (MQ=255)

                                                                                                                                tAACGATGCCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTGGGAATTTc  >  1:189761/1‑140 (MQ=255)

GATGACAGCATCAATGTTTCTGTCAAGCTCAGACATAATATTATTTAATGCCTCAGCTTGCTCGATTGTTCTTGGGAAGCCATCTAATAAAAAGCCTTTTTTTGCATCGTCTTCAGAAATTCTTTCCTTAACGATACCTACAGTCACTTCATCAGGAACTAATTCGCCACGGTCCATATAAGACTTAGCTTCTTTACCTAATTCAGTTTCTTCTTTTATAGCTTTTCTGAACATGTCACCAGTTGAAATGTGGGGTATTGGGAATTTC  >  CP000730/2360664‑2360931

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