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
A23 F59 I1 R1	22	28.7	559496	97.2%	543830	149.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	584,121	G→T	intergenic (+205/‑67)	rplA → / → rplJ	ribosomal protein L1/ribosomal protein L10

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	584,121	0	G	T	94.1%	96.9 / ‑2.1	34	intergenic (+205/‑67)	rplA/rplJ	ribosomal protein L1/ribosomal protein L10
Reads supporting (aligned to +/- strand): ref base G (0/2); new base T (17/15); total (17/17)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAA  >  CP000730/583977‑584249

aCAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTggg                                                                                                                              >  1:30095/1‑149 (MQ=255)

                aaGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCtttttt                                                                                                              <  1:234172/149‑1 (MQ=255)

                                tgtgATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATaaaaaaaaaaaaa                                                                                              <  2:3505/149‑11 (MQ=255)

                                  tgATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAg                                                                                            >  2:242152/1‑149 (MQ=255)

                                               tAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTa                                                                               >  1:174605/1‑149 (MQ=255)

                                                  gACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAAt                                                                            >  1:185193/1‑149 (MQ=255)

                                                   aCAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATg                                                                           >  2:206983/1‑149 (MQ=255)

                                                                   ataACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGAAAAAAAAATTTAAATGGAGGTGTCTGAATGTc                                                           <  2:84008/149‑1 (MQ=255)

                                                                    taACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCt                                                          >  1:10938/1‑149 (MQ=255)

                                                                    taACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCt                                                          >  1:144872/1‑149 (MQ=255)

                                                                       attAAAATTTATCCTGGGGCGGTTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGACTTGGGTAGAAAGTGCTTTTTTTAATAATATAAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCt                                                       <  2:152126/148‑1 (MQ=255)

                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTTTTTTTTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     >  2:132640/1‑149 (MQ=255)

                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  2:154222/149‑1 (MQ=255)

                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  2:276128/149‑1 (MQ=255)

                                                                         tAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                     <  1:232312/149‑1 (MQ=255)

                                                                          aaaaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTAGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATc                                                    <  2:271658/149‑1 (MQ=255)

                                                                            catctATCCTGCCGAGGCTAAAATTGACTTGCACGTGATGCTCTACGATCTTTCAAGCACTTTTTGCCTAGGGCACAAAGAGCTTTTTTTATTAATTCTCAAAAAATCACCAAAAATTTAAATGGTTATGTCGGAATCTCTGCTATCAt                                                  >  2:170201/5‑149 (MQ=255)

                                                                              tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTg                                                <  1:242152/149‑1 (MQ=255)

                                                                                 aTCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAg                                             <  1:111964/149‑1 (MQ=255)

                                                                                 aTCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAg                                             <  2:232428/149‑1 (MQ=255)

                                                                                   ccTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCt                                           >  2:72676/1‑149 (MQ=255)

                                                                                     tGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaa                                         >  1:88106/1‑149 (MQ=255)

                                                                                        cGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaaaaa                                      >  1:133948/1‑149 (MQ=255)

                                                                                        cGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTaaaaa                                      >  1:17398/1‑149 (MQ=255)

                                                                                            gCTAAAATTGACTTGAACGTGATGATCTATGATCTATCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATAAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAaacaa                                  <  2:21148/149‑1 (MQ=255)

                                                                                               aaaaTTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTa                               >  2:214219/1‑149 (MQ=255)

                                                                                                      aCTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgatg                        >  2:142908/1‑149 (MQ=255)

                                                                                                              gtaatgatctatgatctTACAAGCAATTTTTGCCTTGAGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCt                <  2:93795/146‑1 (MQ=255)

                                                                                                                   gatctatgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGt           <  1:261834/149‑1 (MQ=255)

                                                                                                                    atctatgatctTTCAAGCACTTTTTGACTTGGGTAGAAAGTTCTTTTATAAAAAAAAAAAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTa          <  2:257395/149‑1 (MQ=255)

                                                                                                                    atctatgagctTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATAAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTa          <  2:62829/149‑1 (MQ=255)

                                                                                                                         taatcgTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATc     <  2:148283/147‑1 (MQ=255)

                                                                                                                           atctTTCAAGCACTTTTTGCCTTGGTTAGAAAGTGCTTTTTTTATTTTTTTTTAAAAAAGCACCAACAATTTAAATGGCGGTGTCTTAATGTCTGCTATCATTTAAGCTAAAAAACAACTATTTTATGAAATTGCTTATGTACTATCaa   >  2:113442/1‑149 (MQ=255)

                                                                                                                            tctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCaaa  >  1:253341/1‑149 (MQ=255)

ACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAA  >  CP000730/583977‑584249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A