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
A13 F191 I1 R2	32	34.5	741600	95.9%	711194	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,710,898	(T)_6→5	coding (29/1812 nt)	oatA ←	possible acetyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,710,893	0	T	.	86.2%	93.2 / 11.7	29	coding (34/1812 nt)	oatA	possible acetyltransferase
Reads supporting (aligned to +/- strand): ref base T (2/2); new base . (12/13); 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 = 9.57e-01

TAACCTGAAATAACGAAGAATGTATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTAATTGATTTAAC  >  CP000730/2710754‑2711022

tAACCTGAAATAACGAAGAATGTATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACAtt                                                                                                                                  <  2:261772/141‑1 (MQ=255)

             cGAAGAATGTATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGtt                                                                                                                     >  1:78548/1‑141 (MQ=255)

                agaaTGTATCTACCCCTAAAAAGCCCCCCCTTAACCATTGTGCATTCAAGTGATAACTAAAGATTCCTATCACTGCGAACGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTaaa                                                                                                                 <  1:34575/141‑1 (MQ=255)

                  aaTGTATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGt                                                                                                               <  2:118082/141‑1 (MQ=255)

                      tATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCttt                                                                                                           >  2:85148/1‑141 (MQ=255)

                               cTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCAt                                                                                                  >  1:325349/1‑141 (MQ=255)

                                        ccccACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAAGCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATaaa                                                                                         <  2:164675/141‑1 (MQ=255)

                                        ccccACTTAACCATTGGGCATGCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTCTCCATGTTAATaaa                                                                                         <  2:66747/141‑1 (MQ=255)

                                            aCTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGcc                                                                                     >  1:51978/1‑141 (MQ=255)

                                                 aCCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCatt                                                                                >  1:135268/1‑141 (MQ=255)

                                                       gtgCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGTGTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCatttattt                                                                           >  1:108394/1‑141 (MQ=255)

                                                         gCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTtc                                                                        <  1:319971/141‑1 (MQ=255)

                                                           aTTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTtctc                                                                      <  1:848/141‑1 (MQ=255)

                                                                 gTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTAtttt                                                                >  2:235435/1‑141 (MQ=255)

                                                                  tGATAAATAATGATTCCTATAACTGCGAACGCTCCCTGACCAGGGTATCCATTTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTg                                                               <  1:70003/141‑1 (MQ=255)

                                                                             gATTCCTATAACTGCGAATTCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTTTTTTTTTTATCATATcac                                                    >  2:34615/1‑141 (MQ=255)

                                                                             gATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATcac                                                    <  1:98669/141‑1 (MQ=255)

                                                                              aTTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATcaca                                                   <  2:41044/141‑1 (MQ=255)

                                                                               ttCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACaa                                                  >  2:351948/1‑141 (MQ=255)

                                                                                tCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAat                                                 >  1:267493/1‑141 (MQ=255)

                                                                                 ccTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAat                                                 <  2:78548/141‑1 (MQ=255)

                                                                                            gAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGaaaat                                     >  1:124370/1‑141 (MQ=255)

                                                                                            gAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGaaaat                                     >  2:213227/1‑141 (MQ=255)

                                                                                                gCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGaaaataaa                                  <  1:42961/141‑1 (MQ=255)

                                                                                                           aTCTAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGa                      <  2:20224/141‑1 (MQ=255)

                                                                                                              tAATCCAGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGAttt                   <  1:15181/141‑1 (MQ=255)

                                                                                                                    aGGTAAGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTACCCATGTTAGTAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTa             >  1:283108/1‑141 (MQ=255)

                                                                                                                        aaGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTAATTg         <  2:206208/141‑1 (MQ=255)

                                                                                                                         aGTATCGCGGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTAATTGa        >  2:86923/1‑141 (MQ=255)

                                                                                                                               gcgGGGAATACA‑TTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTAATTGATTTAAc  <  1:315896/141‑1 (MQ=255)

TAACCTGAAATAACGAAGAATGTATCTACTCCTAAAAAGCCCCCACTTAACCATTGTGCATTCAAGTGATAAATAATGATTCCTATAACTGCGAATGCCCTCAATCCATCTAATCCAGGTAAGTATCGCGGGGAATACATTTTTTCTAAACGTTTAAAGTCTTTTGTATCCATGTTAATAAACGCCCCATTTATTTTTCTCTATTTTGTAGCATATCACAATATTTTTGAAAATAAAATATTGCACTGATTTTCATTAATTGATTTAAC  >  CP000730/2710754‑2711022

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

GATK/CNVnator alignment

N/A