Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,064,126	G→C	44.7%	Y121* (TAC→TAG)	brpA ←	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)	brpA	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: ‑