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
A19 F74 I1 R1	13	68.8	1581882	91.8%	1452167	133.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,785,994	C→A	intergenic (‑207/+217)	aur ← / ← isaB	M04 family aureolysin/immunodominant antigen B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,785,994	0	C	A	97.1%	99.9 / ‑2.9	34	intergenic (‑207/+217)	aur/isaB	M04 family aureolysin/immunodominant antigen B
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (19/14); total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.05e-01

ATGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAAACA  >  CP000730/2785858‑2786119

aTGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTa                                                                                                                           >  1:124039/1‑141 (MQ=255)

    ttatttctatttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTAtttt                                                                                                                       <  1:173182/141‑1 (MQ=255)

        ttctatttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTtgtg                                                                                                                   >  2:696707/1‑141 (MQ=255)

            atttatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGaaaa                                                                                                               <  2:380584/141‑1 (MQ=255)

               tatttctatACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTTTTTTTTTTTTTTGTAGCTAAATAAAATTTTAAAAATTGAGTTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAatat                                                                                                            >  2:516417/1‑141 (MQ=255)

                       taCTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTTTTTTTTTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTTTCATGTATTTATTTTTGTGTAATTATTaatatat                                                                                                    >  2:534790/1‑136 (MQ=255)

                          tttttGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACa                                                                                                 >  1:431156/1‑141 (MQ=255)

                              tGTTCGTTGATTTTATTTATTGATTCTTCTCTTTTTTAAAAATGTTATCTGTAGCTAAATCAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAAt                                                                                             >  1:457077/1‑141 (MQ=255)

                               gTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATa                                                                                            >  1:760953/1‑141 (MQ=255)

                                           tatttattGATACTTTTCTTTTTTAAAAATGTTTTCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACGAAATAGGGCTCtatata                                                                                <  2:461884/141‑1 (MQ=255)

                                             tttattGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGatttattt                                                                                                                        >  2:73291/1‑99 (MQ=255)

                                             tttattGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACt                                                                              <  2:124039/141‑1 (MQ=255)

                                             tttattGATTCTTGTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGatttattt                                                                                                                        <  1:73291/99‑1 (MQ=255)

                                                      tcttttctttTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGGAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATg                                                                     >  1:533452/1‑141 (MQ=255)

                                                         tttcttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                  >  2:52782/1‑141 (MQ=255)

                                                         tttcttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                  >  1:742340/1‑141 (MQ=255)

                                                            cttttTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGaa                                                               >  2:605095/1‑141 (MQ=255)

                                                              tttttAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAat                                                             >  1:166889/1‑141 (MQ=255)

                                                                 ttAAAAATGTTATCTGTAGCTAAATAAAATTTTAATTATTTTTCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATAtg                                                          >  2:226891/1‑141 (MQ=255)

                                                                         gTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATaa                                                  <  1:34185/141‑1 (MQ=255)

                                                                           tATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACt                                                <  1:19932/141‑1 (MQ=255)

                                                                              cTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                  <  1:422271/120‑1 (MQ=255)

                                                                              cTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCtt                                                                  >  2:422271/1‑120 (MQ=255)

                                                                                       aataaaATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatc                                    <  2:431156/141‑1 (MQ=255)

                                                                                          aaaaTTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatcata                                 >  1:423598/1‑141 (MQ=255)

                                                                                            aaTTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAataatcataat                               <  1:469687/141‑1 (MQ=255)

                                                                                                ttAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCaaa                           >  1:726491/1‑141 (MQ=255)

                                                                                                       ttGAGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATaacaat                    >  2:642664/1‑137 (MQ=255)

                                                                                                          aGCTTAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACGAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACAtttt                 <  2:609086/141‑1 (MQ=255)

                                                                                                              tAATTATATTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATc             <  1:534790/141‑1 (MQ=255)

                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGctc                                                                                      >  2:328616/1‑63 (MQ=255)

                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGctc                                                                                      <  1:328616/63‑1 (MQ=255)

                                                                                                                   atatTTTAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTTAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAAttt        <  1:516417/141‑1 (MQ=255)

                                                                                                                       tttAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCaaa    <  2:457077/141‑1 (MQ=255)

                                                                                                                        ttAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAaac   >  1:607224/1‑141 (MQ=255)

                                                                                                                         tAAAATTTATCAAGGATTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAaaca  >  2:136319/1‑141 (MQ=255)

ATGATTATTTCTATTTATTTCTATACTTTTTGTTCGTTGATTTTATTTATTGATTCTTTTCTTTTTTAAAAATGTTATCTGTAGCTAAATAAAATTTTAAAAATTGAGCTTAATTATATTTTAAAATTTATCAAGGCTTTATTTTTGTGAAAATATTAACAAATACAAAATAGTGCTCTATATACTTAATCAATGCTTGAAATATGTGAGATAACTATTTAAATAATCATAATCAAATAAACATTTTTATCAATTTCAAACA  >  CP000730/2785858‑2786119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A