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
A7 F55 I1 R1	9	17.1	823558	91.9%	756849	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	5,656,850	C→A	G299V (GGT→GTT)	tktA ←	transketolase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,656,850	0	C	A	90.6%	78.5 / 1.6	32	G299V (GGT→GTT)	tktA	transketolase A
Reads supporting (aligned to +/- strand): ref base C (1/2); new base A (18/11); total (19/13)
Fisher's exact test for biased strand distribution p-value = 5.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

TTCGTTGATGTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCACCGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCTTGTT  >  NC_002947/5656708‑5656992

ttCGTTGATGTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCACCggcggc                                                                                                                                         <  1:376787/150‑1 (MQ=255)

 tCGTTGATGTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCATGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGcc                                                                                                                                        >  2:398526/1‑150 (MQ=255)

   gTTGATGTAGGCCTGGGCCTTTTAGCTCCTGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGAAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCtt                                                                                                                                      >  1:76670/1‑150 (MQ=255)

     tGATGTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGCAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTgg                                                                                                                                    <  1:157434/150‑1 (MQ=255)

         gTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATc                                                                                                                                >  2:327647/1‑150 (MQ=255)

                  ggCCTTTTCGCTGAGGGCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGc                                                                                                                       <  2:286963/150‑1 (MQ=255)

                                 gTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCgg                                                                                                        >  2:361883/1‑150 (MQ=255)

                                  tCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCggg                                                                                                       >  1:50492/1‑150 (MQ=255)

                                              tCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGAt                                                                                                                 <  1:329190/128‑1 (MQ=255)

                                              tCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGAt                                                                                                                 >  2:329190/1‑128 (MQ=255)

                                              tCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACggg                                                                                           >  1:15843/1‑150 (MQ=255)

                                                    cTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATCTCGGCCGGGATTTCGAACGGCCCGTgg                                                                                     >  1:392912/1‑150 (MQ=255)

                                                         aCGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCACCGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCa                                                                                >  1:127305/1‑150 (MQ=255)

                                                                   aaCTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCACCCTTGGCAACGGCGGGCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTGTAACGGGCCGGGGTTGCAGTTCAggtac                                                                      >  1:127909/1‑147 (MQ=255)

                                                                      tCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTgg                                                                   >  1:92511/1‑150 (MQ=255)

                                                                         gCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCgg                                                                <  2:92511/150‑1 (MQ=255)

                                                                         gCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCgg                                                                <  1:361883/150‑1 (MQ=255)

                                                                         gCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCAACTCGGCTTCAACCTTGGCAACGGCGGCCGTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCgg                                                                >  1:51211/1‑150 (MQ=255)

                                                                                 cTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGc                                                        >  1:9267/1‑150 (MQ=255)

                                                                                           gCCTTGGTGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTtcgtcg                                              >  1:78741/1‑150 (MQ=255)

                                                                                              ttGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTg                                           <  1:58798/150‑1 (MQ=255)

                                                                                               tGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCACCGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGc                                          <  2:127305/150‑1 (MQ=255)

                                                                                                      ggCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTgg                                                                                     >  1:337171/1‑100 (MQ=255)

                                                                                                      ggCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTgg                                                                                     <  2:337171/100‑1 (MQ=255)

                                                                                                                     gTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAggg                                                         >  2:286527/1‑113 (MQ=255)

                                                                                                                     gTTCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAggg                                                         <  1:286527/113‑1 (MQ=255)

                                                                                                                      ttCCACTCGGCTTCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCt                   >  2:350164/1‑150 (MQ=255)

                                                                                                                                  tCAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGc       <  2:51211/150‑1 (MQ=255)

                                                                                                                                   cAACCTTGGCAACGGCGTACTTCGCTTCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTACTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCt      <  1:398526/150‑1 (MQ=255)

                                                                                                                                   cAACCTTGGCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGACGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCt      >  1:45680/1‑150 (MQ=255)

                                                                                                                                           gCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCTTGtt  >  2:283827/1‑146 (MQ=255)

                                                                                                                                           gCAACGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCTTGtt  <  1:283827/146‑1 (MQ=255)

TTCGTTGATGTAGGCCTGGGCCTTTTCGCTGAAGTCGGCCGGCAGCTCGCCGCTGGCACGGCGCTTGAACTCGGCAGCCAGCTCCGGGTAGGCCTTGGCGTAGGCGTCGAAGCGCTGGTTCCACTCGGCTTCAACCTTGGCACCGGCGGCCTTGGCATCCCACTCGGCGTAGATGTCGGCCGGGATTTCGAACGGGCCGTGGTTCCAGTTCAGGGCCTGGCGGGTCAGGGCGATTTCGTCGTTGCCCAGCGGGGCACCGTGGCAGTCTTCCTTGCCCTGCTTGTT  >  NC_002947/5656708‑5656992

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