Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,185,073	G→T	9.3%	intergenic (‑117/+317)	yhgF ← / ← fliA	S1 domain RNA‑binding protein/DNA‑directed RNA polymerase sigma subunit FliA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,185,073	0	G	T	9.3%	134.8 / 3.9	43	intergenic (‑117/+317)	yhgF/fliA	S1 domain RNA‑binding protein/DNA‑directed RNA polymerase sigma subunit FliA
Reads supporting (aligned to +/- strand):  ref base G (23/16);  new base T (2/2);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

CAATTGATTGTCCATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTAAAACGACAATTAGATATCTTCTTC  >  CP000730/2184942‑2185213                                                                                                                                    |                                                                                                                                              cAATTGATTGTCCATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCa                                                                                                                                      >  2:313959/1‑141 (MQ=255)     tgattgTCCATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACt                                                                                                                                  >  1:305434/1‑141 (MQ=255)       attgTTCATTTACTTAACCCACACTTTTTATTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACtat                                                                                                                                <  2:398676/141‑1 (MQ=255)         tgTCCATTTACTTAACCCACACTTTTTCTTATATTTACTCATTTATTTTAGCATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGCCTGATTAggaaaaactctat                                                                                                                              >  2:177784/1‑130 (MQ=255)         tgTCCATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTata‑t                                                                                                                             <  1:413667/141‑1 (MQ=255)            ccATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑tttt                                                                                                                          >  1:292799/1‑141 (MQ=255)               tttACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTaaa                                                                                                                       >  1:148813/1‑141 (MQ=255)                ttACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTaaaa                                                                                                                      >  1:383500/1‑141 (MQ=255)                   cTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGc                                                                                                                   <  1:125070/141‑1 (MQ=255)                       aCCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTa                                                                                                               >  1:389183/1‑141 (MQ=255)                           acacTTTTTCTTTAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGat                                                                                                           >  2:142648/1‑141 (MQ=255)                            cacTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGatt                                                                                                          <  1:436244/141‑1 (MQ=255)                            cacTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGatt                                                                                                          <  2:126642/141‑1 (MQ=255)                              cTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGattat                                                                                                        <  1:192214/141‑1 (MQ=255)                                                        ttAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATTATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTaa                                                                              >  1:343813/1‑141 (MQ=255)                                                        ttAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATTATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTaa                                                                              >  1:365728/1‑141 (MQ=255)                                                          aaCATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAAt                                                                            >  2:133128/1‑141 (MQ=255)                                                          aaCATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAAt                                                                            >  1:16400/1‑141 (MQ=255)                                                               atTCTAAAAAACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTTCAAAACATTCAAAACGAATGACTAGGTCATACTATA‑TTTTAAATCGCACTAAGATTATTGAAAATGACACATCGTCATTTCTAAATTTCAt                                                                       <  2:30731/141‑1 (MQ=255)                                                                  cTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAAt                                                                    >  1:285165/1‑141 (MQ=255)                                                                    aaaaTACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCGTCATTTCTAAATTTCATAATCt                                                                  >  2:217649/1‑141 (MQ=255)                                                                    aaaaTACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAGTCt                                                                  >  1:327198/1‑141 (MQ=255)                                                                      aaTACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTaa                                                                >  1:5326/1‑141 (MQ=255)                                                                           ttCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATATTTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGact                                                            >  2:270498/1‑141 (MQ=255)                                                                             cTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATAACACACCATCATTTCTAAATTTCATAATCTAAAactact                                                         >  2:143909/1‑141 (MQ=255)                                                                              tATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATTATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACtt                                                        <  1:96530/141‑1 (MQ=255)                                                                              tATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATTATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACtt                                                        <  1:368259/141‑1 (MQ=255)                                                                                 tAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACttttt                                                     <  1:249414/141‑1 (MQ=255)                                                                                  aaGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACtttttt                                                    <  1:431697/141‑1 (MQ=255)                                                                                   aGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACttttttt                                                   <  2:217672/141‑1 (MQ=255)                                                                                               tAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCa                                       >  2:423864/1‑141 (MQ=255)                                                                                                      aTTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCAcc                                >  1:278177/1‑141 (MQ=255)                                                                                                       ttttCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCt                               <  1:344834/141‑1 (MQ=255)                                                                                                            aCTTCCAAAACATTTAAAACAAATGATTAGGTCAAACTAAA‑ATTTAAAACGCACTAAGATTATTAAAAATGAAACACCATCAATACTAAATTTCATAAACTAAGACTACTTTTTTTATACTAATAGCAAACAACCTATTTa                          >  2:236759/1‑141 (MQ=255)                                                                                                             cTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTaa                         >  2:424967/1‑141 (MQ=255)                                                                                                              ttCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTaaa                        <  1:292071/141‑1 (MQ=255)                                                                                                              ttCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTaaa                        <  1:292039/141‑1 (MQ=255)                                                                                                               tCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATATCAACCCACCTATTTaaaa                       >  2:264778/1‑141 (MQ=255)                                                                                                               tCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTaaaa                       <  2:67327/141‑1 (MQ=255)                                                                                                                 cAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTAAAACg                     <  2:12799/141‑1 (MQ=255)                                                                                                                         ttAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTTTTTTATTTGCAACCCACCTATTTAAAACGACAATTAg             >  2:83318/1‑141 (MQ=255)                                                                                                                           aaaaCGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTCAAAACGACAATTAGat           >  2:403491/1‑141 (MQ=255)                                                                                                                                 aaTGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTAAAACGACAATTAGATAtcttc     <  1:46775/141‑1 (MQ=255)                                                                                                                                    gATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTAAAACGACAATTAGATATCttcttc  <  1:269198/141‑1 (MQ=255)                                                                                                                                    |                                                                                                                                              CAATTGATTGTCCATTTACTTAACCCACACTTTTTCTTAAATTTACTCATTTATTTTAACATATTCTAAAATACTTCTATTAAGGTATGATACTTAATGTAATTTTCACTTCCAAAACATTTAAAACGAATGATTAGGTCATACTATA‑TTTTAAAACGCACTAAGATTATTGAAAATGACACACCATCATTTCTAAATTTCATAATCTAAGACTACTTTTTTTATTCTAATAGCAACCCACCTATTTAAAACGACAATTAGATATCTTCTTC  >  CP000730/2184942‑2185213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑