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 F109 I1 R1	27	23.1	511165	92.8%	474361	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	225,004	G→T	E31* (GAA→TAA)	murQ →	possible sugar phosphate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	225,004	0	G	T	92.9%	65.0 / ‑4.3	28	E31* (GAA→TAA)	murQ	possible sugar phosphate isomerase
Reads supporting (aligned to +/- strand): ref base G (1/1); new base T (10/16); total (11/17)
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

GCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAGGTTGGGT  >  CP000730/224866‑225138

gCCGCATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCGTTAATTACGATGAataaataa                                                                                                                                      >  2:284883/1‑141 (MQ=255)

gCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCCTCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAataaataa                                                                                                                                      >  2:458100/1‑141 (MQ=255)

                    ttCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGCCCCGTTAGc                                                                                                                  >  2:75052/1‑141 (MQ=255)

                     tCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCa                                                                                                                 <  2:429091/141‑1 (MQ=255)

                       agaaaaCTAGGGAGTGGAAGAAGTGATGGAAAGTCGTCCGCCCGAAGCGCTGTATGAAGCGACGATGCCTCTTGAAGTAATGAGTGGTGGAGAGGCTTTAATTACGCTGAATAAATAAGATCAGCAAGTCCCGTTAGCAGt                                                                                                               <  2:201748/139‑1 (MQ=255)

                        aaaaaCTAGGGAGTGTAAGAAGTGAGGGAAAATAGTACGACCGAGGGTTGTAATGAAGCTACGAGGCAGCGTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGtt                                                                                                              <  2:424862/141‑1 (MQ=255)

                         aaaaCTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGACAGTCCCGTTAGCAGTTc                                                                                                             >  2:47780/1‑141 (MQ=255)

                           aaCTAGGGAGGTTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCGTCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGa                                                                                                           <  2:360091/141‑1 (MQ=255)

                                gggAGTGTAAGGAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATACATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGc                                                                                                      <  2:419901/141‑1 (MQ=255)

                                     ggtAAGAAGTGATGGAAAACAGTACGACCGAAGCGCGTAACGAACGCACGCTGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGCCCCGTTAGCAGTTCGAAAGGCAATAc                                                                                                 <  2:176013/140‑1 (MQ=255)

                                      gtAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATAcc                                                                                                <  2:151433/141‑1 (MQ=255)

                                             gggATGGAAAATAGTACGACCGAATCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTg                                                                                         <  2:200805/139‑1 (MQ=255)

                                             gTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCAGCTTGATGAAATGACTGTGGAAGAGGCTGTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTg                                                                                         <  2:299823/141‑1 (MQ=255)

                                               gagggAAAATAGTACGACATAAGCGCGTAATTAAGCGACGATGCAGCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTgtc                                                                                       <  2:130466/138‑3 (MQ=255)

                                                        tAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAAt                                                                              >  2:492179/1‑141 (MQ=255)

                                                         aGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGCCTGGGGAAGAGGCTTTAATGACGATGACTAAATAGGTTCAGCAACTCCCGTTAGCAGTTCGAAAGGCAAGCCCACAATTGAGAAAAggactt                                                                             >  2:419862/1‑136 (MQ=255)

                                                         aGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATGAGATCAGCAAGGCCCGTTAGCAGTTCGAAAGGCAATACCAAAATTGACAAAAGCAAta                                                                             >  2:9210/1‑140 (MQ=255)

                                                            aCGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTaaa                                                                          >  2:418674/1‑141 (MQ=255)

                                                              gcacggaGCGCGTAATGAAGCGAAGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTaaaaa                                                                        <  2:346669/135‑1 (MQ=255)

                                                              gaacggaGCGAGTAATGAAGCGAGGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTaaaaa                                                                        <  2:221610/135‑1 (MQ=255)

                                                              gACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTaaaaa                                                                        <  2:418769/141‑1 (MQ=255)

                                                                        cgTAATGAAAGGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGGCAAAAGTAATTAAAAAAACAATTgta                                                              >  1:8509/1‑139 (MQ=255)

                                                                         gTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATACATAACATCAGCAAGTCCCGTTAGCGGTTCGAAAGGCACTACAACAATTGACAAACGTACTTAACAAACCAATTGcac                                                             >  2:428788/1‑141 (MQ=255)

                                                                            aTGAAGCGACGATGCATCGTGATGAAAGGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAATCTATTGCACAGt                                                          <  2:481796/141‑1 (MQ=255)

                                                                                   gacgaTGCATCTTGATGAAATGACTTTGGAAGAGGCTTCAATTACGATGAATAAATAATATCAGCACGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGGCAAAAGTCATTAAAAAAACAATTGCACAGTATaaaaa                                                   <  2:371198/141‑1 (MQ=255)

                                                                                      gaTGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAggg                                                >  2:307341/1‑141 (MQ=255)

                                                                                       aTGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAgggg                                               >  2:465767/1‑140 (MQ=255)

                                                                                        tGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGGATAAAAAGGGTg                                              >  2:157106/1‑141 (MQ=255)

                                                                                             cTTGAGGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACga                                         <  2:386320/141‑1 (MQ=255)

                                                                                                        gACTGGGCAAGAGGCTTTAATTACGATGAATAAATAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCATAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTatat                              <  2:336089/141‑1 (MQ=255)

                                                                                                                                    aataaataAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGAGAAAAGTAATCAAAAAAACAATTGCACAGTATAAAAAGGGGGGACGATTGATTTATATCGGTGCAGGTACAAGAGGAAGGTTgggg  >  2:35906/1‑140 (MQ=255)

                                                                                                                                    aataaataAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAGGTGGGgt  >  2:395977/1‑141 (MQ=255)

GCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGATGGAAAATAGTACGACCGAAGCGCGTAATGAAGCGACGATGCATCTTGATGAAATGACTGTGGAAGAGGCTTTAATTACGATGAATAAAGAAGATCAGCAAGTCCCGTTAGCAGTTCGAAAGGCAATACCACAATTGACAAAAGTAATTAAAAAAACAATTGCACAGTATAAAAAGGGTGGACGATTGATTTATATCGGTGCAGGTACAAGTGGAAGGTTGGGT  >  CP000730/224866‑225138

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