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 F121 I1 R1	25	27.5	612106	95.4%	583949	136.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,064,016	G→A	A158V (GCA→GTA)	brpA ←	LytR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,064,016	0	G	A	96.5%	94.3 / ‑3.9	29	A158V (GCA→GTA)	brpA	LytR family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (18/10); total (19/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

AGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGG  >  CP000730/1063883‑1064143

aGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCat                                                                                                                          >  2:95296/1‑141 (MQ=255)

            aTTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTcac                                                                                                              <  2:80603/141‑1 (MQ=255)

                  tttttGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACataata                                                                                                        >  2:241648/1‑141 (MQ=255)

                          aCCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAg                                                                                                >  1:196389/1‑141 (MQ=255)

                           cccTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTTACTCTCACATAATAATCAACAgg                                                                                               >  2:298257/1‑141 (MQ=255)

                             cTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTa                                                                                             <  2:113963/141‑1 (MQ=255)

                                       tttaatCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGt                                                                                   >  1:82931/1‑141 (MQ=255)

                                              ttACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCt                                                                            >  2:105447/1‑141 (MQ=255)

                                               tACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCtc                                                                           >  1:256518/1‑140 (MQ=255)

                                               gaCCAGTATCATCTGGGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGTGACATTCATGGTAGCTTTTa                                                                           >  2:138601/2‑141 (MQ=255)

                                                          tcTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCAtt                                                                <  1:124668/141‑1 (MQ=255)

                                                                     ttCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTgg                                                     >  2:178748/1‑141 (MQ=255)

                                                                     ttCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTgg                                                     <  1:83018/141‑1 (MQ=255)

                                                                        aTTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGacc                                                  <  1:230826/141‑1 (MQ=255)

                                                                             aGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGAccacca                                              <  2:88606/140‑1 (MQ=255)

                                                                             aGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGAccacca                                              >  1:88606/1‑140 (MQ=255)

                                                                                 gTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAtgc                                         >  1:93044/1‑141 (MQ=255)

                                                                                  tATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAtgca                                        <  1:95296/141‑1 (MQ=255)

                                                                                  tATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAtgca                                        >  2:218957/1‑141 (MQ=255)

                                                                                         tatactatgatgtGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAtgcatgtgcat                                 >  1:130354/13‑141 (MQ=255)

                                                                                          atcatAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATACTTTCATGTTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAtgcatgtgcatg                                >  1:234093/1‑141 (MQ=255)

                                                                                                       ccaccaAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTa                                                                                             <  2:140089/67‑1 (MQ=255)

                                                                                                       ccaccaAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTa                                                                                             >  1:140089/1‑67 (MQ=255)

                                                                                                       ccaccaAGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCg                   >  2:170196/1‑141 (MQ=255)

                                                                                                       ccaccaAGCTCATTTACAGCCTAGACAAATAATTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCTATTGCGGCAATTGGACTACCATATGCATGTGCATGGGTAATATTATCg                   >  2:44294/1‑141 (MQ=255)

                                                                                                             aGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAg             <  1:38912/141‑1 (MQ=255)

                                                                                                             aGCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAg             >  2:166811/1‑141 (MQ=255)

                                                                                                              gCTCATTTACAGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGc            >  2:7254/1‑141 (MQ=255)

                                                                                                                        aGCCTCGACAAATACTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAgg  <  1:281601/141‑1 (MQ=255)

AGCCTCATCACCATTTAATTTTTGGTACCCTTTTTTAATTTTAATCTTACCAGTATCATCTGTGTTAGGTTCATTTAAGTCGTATGGCACATCATAGTATATGCCACCAAGCTCATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGG  >  CP000730/1063883‑1064143

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A