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
A2 F13 I0 R1	203	85.6	3649704	98.8%	3605907	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	4,952,675	T→G	33.4%	intergenic (‑122/+35)	fliL ← / ← fliK	flagellar protein FliL/flagellar hook‑length control protein FliK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,952,675	0	T	G	33.4%	13.4 / 12.3	24	intergenic (‑122/+35)	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
Reads supporting (aligned to +/- strand): ref base T (7/8); new base G (6/2); total (14/10)
Fisher's exact test for biased strand distribution p-value = 3.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

CTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCG  >  NC_002947_CJ‑RC/4952538‑4952821

cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaag                                                                                                                                         <  8:166665/149‑1 (MQ=255)

cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaag                                                                                                                                         <  4:7523/149‑1 (MQ=255)

cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaa                                                                                                                                          <  1:452710/148‑1 (MQ=255)

cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaa                                                                                                                                          <  1:253865/148‑1 (MQ=255)

   cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                       <  1:27922/148‑1 (MQ=255)

   cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                       <  2:176481/148‑1 (MQ=255)

   cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                       <  3:200174/148‑1 (MQ=255)

   cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                       <  3:53440/148‑1 (MQ=255)

        ttCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGAAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGATTCATCGCGGGGGCGCCCCCGCAAAaggcaac                                                                                                                                 >  7:389746/1‑147 (MQ=255)

           gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTGTTGGCGGGGGCGGCCGCGCTGAagcccccccc                                                                                                                              >  7:347836/1‑143 (MQ=255)

           gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTAATAGCGGGGGGGGCCCCGCAGAagcccccccc                                                                                                                              >  7:129745/1‑143 (MQ=255)

                   aataatCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTGATAGCGGGGGGGCCCGCGCAGAAACCACCCCACGccca                                                                                                                        >  6:312862/1‑145 (MQ=255)

                                       gggTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTAGCGGGCTCGCCCGCGAAGAAGCCCCCCCAGGCCAACACTTATAAGGCGGAGTAAtag                                                                                                  >  6:85450/1‑147 (MQ=255)

                                                          ttggcttgAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCACGCCCGCGAAGAAGCCCGCCCAGGCCAACAGTTATAAGGCGTAGTAATCGACCGCACAGTCGCCGACaa                                                                               >  8:225577/1‑149 (MQ=255)

                                                              cttgAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGATTTGCGGTGCTGGCTTCTTAGCCGGGGCGCCCGCGGAGGAACCACCCCCGGCCAAAAGATTTAAAGCGGATTTATAGACCGCACAGTAGCCGACcaccac                                                                           >  8:454533/1‑149 (MQ=255)

                                                                                                      ccAGCTGGTTTTGGGGGGCGGGCTTCTGCGGGGGCTCGCCGGCTAATAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGc                                    <  6:323821/148‑1 (MQ=255)

                                                                                                                         tGGCTTATGCGGGGGCTCCCCGGCCAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGgc                <  6:50226/149‑1 (MQ=255)

                                                                                                                           gCTTCTTCGCGGGCTAGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATAAGGCGTAGTAATAGACCGCACAGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATAGACCGCTTCGGCCCCACCCTGCAAGGCCCCgcgc              >  8:272429/1‑149 (MQ=255)

                                                                                                                             ttcttcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCCgcgcgc            >  3:176395/1‑149 (MQ=255)

                                                                                                                              tcttcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCCCCCTGCTCGGCCCGGCGcgcc           >  2:455307/1‑149 (MQ=255)

                                                                                                                                 tcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccgc         >  1:301360/1‑148 (MQ=255)

                                                                                                                                 tcGCGGGCGAGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCgccgcc        >  5:86751/1‑149 (MQ=255)

                                                                                                                                   gcgGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCAc      >  2:38023/1‑149 (MQ=255)

                                                                                                                                       gCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCg  >  6:99832/1‑149 (MQ=255)

CTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCG  >  NC_002947_CJ‑RC/4952538‑4952821

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A