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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,064,126	G→C	44.7%	Y121* (TAC→TAG)	USA300HOU_1000 ←	LytR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,064,126	0	G	C	44.7%	‑4.4 / 34.2	27	Y121* (TAC→TAG)	USA300HOU_1000	LytR family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (9/6); new base C (6/6); total (15/12)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.35e-01

CATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTT  >  CP000730/1063996‑1064258

cATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCaa                                                                                                                            >  2:199442/1‑141 (MQ=255)

          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCTAAATTTAGGAAt                                                                                                                  >  1:101584/1‑141 (MQ=255)

          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAAt                                                                                                                  >  1:121274/1‑141 (MQ=255)

          cTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAAt                                                                                                                  >  1:117366/1‑141 (MQ=255)

               cAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCACATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGc                                                                                                             <  1:122944/141‑1 (MQ=255)

                        tCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTAt                                                                                                    >  1:199413/1‑141 (MQ=255)

                              tGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTg                                                                                              <  2:111306/141‑1 (MQ=255)

                              tGACCCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTg                                                                                              <  2:48311/141‑1 (MQ=255)

                               gACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTgg                                                                                             >  1:224754/1‑141 (MQ=255)

                                                 aaCAGGTACATTCATTGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAAt                                                                           >  2:209595/1‑141 (MQ=255)

                                                        aaaTTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATAGGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGAAAATATCACGTGGAATACTAAGCATCTTAATTGGCTGt                                                                    >  2:185817/3‑141 (MQ=255)

                                                              aTGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTttgat                                                              <  1:228168/141‑1 (MQ=255)

                                                                    gCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTa                                                        >  1:263015/1‑141 (MQ=255)

                                                                          ccctaaTCCATTGCCGCAATTGGACCACCATCTGCATGTGCATGGGTAATCTTATCCTAATAGTCAACTTTAGGAATGTAGCTGATAGTATCAACTGGAATACTAAGCATTTTAATTTGATGTTTTGATTGATTAAAagta                                                  <  2:196012/137‑1 (MQ=255)

                                                                                  cATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAAt                                          <  1:70963/141‑1 (MQ=255)

                                                                                    ttGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCa                                        >  2:36910/1‑141 (MQ=255)

                                                                                     tGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCAt                                       <  1:223029/141‑1 (MQ=255)

                                                                                      gCGGCAATTGGACCACCAAACCAGCCTTTATGGGTAATCTTATCCTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATa                                      >  2:270483/1‑141 (MQ=255)

                                                                                       cGGCCATTGGACCACCATATGCATGTGCATGGGTAATCTTATGGGAATAGCCAACTGTAGGAATGTAGCTGATAGTATCACGAGGAATACTAAGCATTCTAATTTGATTTGTTGATTGATTAAAAGTAGTTAAAATCATAg                                     <  2:101584/141‑1 (MQ=255)

                                                                                       cGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAg                                     <  2:121274/141‑1 (MQ=255)

                                                                                            aTTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTCAGCATCCTAATTTGATGTTTTGATTGATTAAAAGTAGTTCAAATCATACCGCCt                                >  2:164834/1‑141 (MQ=255)

                                                                                                 accaccATATGCATGTGCATGGATAATCTTATCGTAATAGCCAACTTTAGGAATTTAGCTGATAGGATCACGGGGAATACTAAGCATTGTAATTTGCTGTTTTTATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCt                           >  2:209333/1‑141 (MQ=255)

                                                                                                        tatGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAgtgt                    <  1:199442/141‑1 (MQ=255)

                                                                                                                   atgGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTg         >  1:159923/1‑141 (MQ=255)

                                                                                                                     gggTAATATTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCATGTc       >  2:33142/1‑141 (MQ=255)

                                                                                                                       gTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATGTGATGTTTAAATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCt     <  1:121525/141‑1 (MQ=255)

                                                                                                                          aTCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCtttt  <  1:209595/141‑1 (MQ=255)

CATTTACAGCCTCGACAAATGCTTTCATATTGACTCTCACATAATAATCAACAGGTACATTCATGGTAGCTTCTACCGAATCCATTGCGGCAATTGGACCACCATATGCATGTGCATGGGTAATCTTATCGTAATAGCCAACTTTAGGAATGTAGCTGATAGTATCACGTGGAATACTAAGCATTCTAATTTGATGTTTTGATTGATTAAAAGTAGTTAAAATCATAGCGTCTGATCTAGAGTGTTCAGCATCCTGTCCTTTT  >  CP000730/1063996‑1064258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A