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
A20 F48 I1 R1	52	61.9	2103308	98.8%	2078068	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	288,809	G→T	G118G (GGC→GGA)	xynR ←	CP4‑6 prophage; DNA‑binding transcriptional repressor XynR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	288,809	0	G	T	91.7%	74.0 / ‑1.1	24	G118G (GGC→GGA)	xynR	CP4‑6 prophage; DNA‑binding transcriptional repressor XynR
Reads supporting (aligned to +/- strand): ref base G (2/0); new base T (12/10); total (14/10)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTGCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCGAATATCGATGGA  >  NC_000913/288680‑288931

gtACTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTGCCTTCAAtct                                                                                                                  >  1:499692/1‑140 (MQ=255)

   cTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAAtcttct                                                                                                               <  1:432932/140‑1 (MQ=255)

   cTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAAtcttct                                                                                                               <  1:848520/140‑1 (MQ=255)

   cTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAAtcttct                                                                                                               <  1:828392/140‑1 (MQ=255)

     gATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCg                                                                                                             >  2:818863/1‑140 (MQ=255)

           ccTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGAGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAg                                                                                                       >  1:971568/1‑140 (MQ=255)

             tCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTTCATATacac                                                                                                     >  2:208491/1‑140 (MQ=255)

             tCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGGGGCGTGCACCGGCAGGCGGCGGCCGATGCGCTAATAGGCGATGGCGGGCAGCTTTACTTTAATCTTCTCCATATAGAc                                                                                                     >  2:104464/1‑140 (MQ=255)

                agcagGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGAcccc                                                                                                  >  1:927918/1‑140 (MQ=255)

                     ggCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCCGCCGATGCGTGAATAGGCGATTGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCAc                                                                                             >  2:1015352/1‑140 (MQ=255)

                       cGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGc                                                                                           <  1:104464/140‑1 (MQ=255)

                              cTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCa                                                                                    <  1:121244/140‑1 (MQ=255)

                                           agccagGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATg                                                                       <  2:902458/140‑1 (MQ=255)

                                               agGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGggtg                                                                   <  2:790731/140‑1 (MQ=255)

                                                              tGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGCCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGGCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTccgc                                                    >  1:15803/1‑140 (MQ=255)

                                                               gCCGATGGCGGTGGCGTGCACCGGTAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTccgcc                                                   >  1:236571/1‑140 (MQ=255)

                                                               gCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTccgcc                                                   >  2:180210/1‑140 (MQ=255)

                                                               gCCGATGGCGGTGGCGTGCACCGGCACGCGGCGGCCGATGCGGGAATAGGCGATGGCGGCCAGCTTGCCTTTAATCTTCTCGATATAGACCCCTTTACGCCCGTTCAGGATCCCCAGATGGGTGGTCTGCCCGGTccgcc                                                   >  1:320959/1‑140 (MQ=255)

                                                                  gATGGCGGTGGCGTGCACCGGCAGGCGGCGGCAGAGGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCCTCTCGATATAGTTCCCTTCACGCCCGTCCAGGATCCCAAGATGGGTGGTCGGCCCGGTCCGCCggg                                                <  2:971568/140‑1 (MQ=255)

                                                                                 cACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTcagcc                                 <  1:208491/140‑1 (MQ=255)

                                                                                 cACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTcagcc                                 >  2:758662/1‑140 (MQ=255)

                                                                                      gCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCt                            >  1:192893/1‑140 (MQ=255)

                                                                                              cggcCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCtt                    >  1:825212/1‑140 (MQ=255)

                                                                                              cggcCGATGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCtt                    <  1:758662/140‑1 (MQ=255)

                                                                                                    aTGCGTGAATAGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCg              >  2:763235/1‑140 (MQ=255)

                                                                                                              aGGCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCGAATATCGATg    <  2:10274/140‑1 (MQ=255)

                                                                                                                gCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCGAATATCGATGGa  >  1:977483/1‑140 (MQ=255)

                                                                                                                gCGATGGCGGCCAGCTTTCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCGAATATCGATGGa  >  2:198965/1‑140 (MQ=255)

GTACTGATAGCCCTCCAGCAGGGCGTTCAGCTCGGCCTCGCCCAGCCAGGCAATCAACACCTTGCCGATGGCGGTGGCGTGCACCGGCAGGCGGCGGCCGATGCGTGAATAGGCGATGGCGGCCAGCTTGCCTTCAATCTTCTCGATATAGACCCCTTCACGCCCGTCCAGGATCCCCAGATGGGTGGTCTGCCCGGTCCGCCGGGACAGCTCCGTCAGCCAGCCTTTTGCCTTCTGCCGAATATCGATGGA  >  NC_000913/288680‑288931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A