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 I0 R1	75	33.7	751148	92.2%	692558	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	584,121	G→T	100%	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	96.8%	89.3 / ‑5.9	33	intergenic (+205/‑67)	rplA/rplJ	ribosomal protein L1/ribosomal protein L10
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (16/15); minor base A (1/1); total (17/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCA  >  CP000730/583984‑584253

gTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTACGAGTTACCTATAACTTAAAAGTTATCCTGCCGAGGATAAAATTGAATTGAACGTGATGATCCATGATCTTTCAAGCATTTTTTGCCTTgg                                                                                                                                   >  2:60072/1‑141 (MQ=255)

     tttcAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGa                                                                                                                              <  1:346505/138‑1 (MQ=255)

                 ttACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGGGGCTAAAATTGATTTGAACGTGATAAGCAATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCtttttt                                                                                                                  >  2:6480/1‑141 (MQ=255)

                 ttACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCtttttt                                                                                                                  >  2:368683/1‑141 (MQ=255)

                         tgtgATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAAtt                                                                                                          <  1:368683/141‑1 (MQ=255)

                            gATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTa                                                                                                       >  2:60013/1‑141 (MQ=255)

                             attattTTACCTAAGAAAGTAAGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTaa                                                                                                      >  1:190568/1‑141 (MQ=255)

                                      tcTAAGAAAGTAGGAGTTATTTATAACTTAAAATGTAGCCGGCCGAGAAAAAAAAAAAAATGAACGAGATGAGATATGATCTTTCAAGCACTCTTTGCCTAAGGTAGAAAGTGCTTTTTTTTTTTATTTTaaaaaaaaaaa                                                                                             <  2:352682/140‑5 (MQ=255)

                                                tAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTa                                                                                   >  1:163146/1‑141 (MQ=255)

                                                        atttatAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTTTTATTTTTAAAAAAAACACCAACAATTGAAGTGGCgg                                                                           >  2:341426/1‑141 (MQ=255)

                                                               aCTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGa                                                                    <  2:98172/141‑1 (MQ=255)

                                                               aCTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTAAAGTTGCGGTGTCGGa                                                                    >  1:224345/1‑141 (MQ=255)

                                                                 ttAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAGGCACCAAAAATTTAAATGGAGGTGTCTGAAt                                                                  >  1:181210/1‑141 (MQ=255)

                                                                    aaaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTc                                                               <  2:340680/141‑1 (MQ=255)

                                                                     aaTTTATCCGGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCt                                                              <  1:108045/141‑1 (MQ=255)

                                                                          aTCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                         >  2:333977/1‑141 (MQ=255)

                                                                                   gggCTAAAATTGACTTGAACGTGAGGATCTATGATCTTTCAAGCACTTTTTGCGAAGGACAAAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGc                                                <  1:177060/140‑1 (MQ=255)

                                                                                   aGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGc                                                <  1:281044/141‑1 (MQ=255)

                                                                                    ggCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCt                                               <  2:347299/141‑1 (MQ=255)

                                                                                    ggCTAAAATTGACTTGAACGTGAGGATCTATGATCTTTCAAGCAATTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCt                                               <  2:1120/141‑1 (MQ=255)

                                                                                           aTTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTCAAAaac                                        >  1:156648/1‑141 (MQ=255)

                                                                                                cTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTTTTTTTTTTTTAAAGTGCTTTTTTTATTAATTTTAAAAAAAGTGTCAAAAATTTAGATGTAGGTGTCTGTATGTCTTCTATCATTTACTCTATAAAATAACTa                                   >  2:47666/1‑141 (MQ=255)

                                                                                                cTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAACACCAAAAATATAAATAGAGGTGTCTGAATGTATGAGTTCATTGAAGATCAAAAAACACTa                                   >  2:64609/1‑141 (MQ=255)

                                                                                                      ggTGATGATCTATGGTCTTTCAAGCAGTTTTTGCCTTGGGGAGAAAGTGGTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgat                             <  2:301219/140‑1 (MQ=255)

                                                                                                      cggtatgatctatgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgat                             <  2:301264/137‑1 (MQ=255)

                                                                                                       gTGATGATCTATGATCTTTCAAGCACTTTTTTTTTTTTTTTTAAACAGCTTTTTTTATTAATTTTAAAAAAAGGACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTtgatg                            >  2:79225/1‑141 (MQ=255)

                                                                                                         gatgatCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGaa                          <  1:60013/141‑1 (MQ=255)

                                                                                                           tgatctaagatatTTCAAGCACTTTTTGTATTGGGTAGAAAGTGTTTTTTTTATTAATCTTAAAAAACGCACCAAAAAATTAAATGTAGGTGTCTGCTTGTCTGCTATAAAAAAAAAAAAAAAACAACTAGTTGATGAAAt                        <  2:314361/141‑1 (MQ=255)

                                                                                                                    atctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGt               <  1:140677/141‑1 (MQ=255)

                                                                                                                     tctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGCAGCTAAAAANCAANTNGTTGATGAAATTGCTGAGGTa              >  1:267267/1‑141 (MQ=255)

                                                                                                                               aCTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCCCGAAACCTCTCAACGGATTTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAAtt    <  1:86459/141‑1 (MQ=255)

                                                                                                                               aCTATTTGCCATGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAGATTTAAATGGAGGAGACCGAAAGACTGCAACCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGTAACTATCaaaat    >  2:184665/1‑139 (MQ=255)

                                                                                                                                 tttttGCCTTGGGAAGAAAGTGCTTTTTTTATTAGTTTTAAAAAAAGCACCAAAAATGTAAATGGAGGTGTCTGAATGTATGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGTTGAGGTACTAGCAAGTTCa  >  1:312935/1‑141 (MQ=255)

GTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATTTTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCA  >  CP000730/583984‑584253

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