Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,389,812	Δ1 bp	intergenic (‑149/+4151)	tldD ← / ← cafA	TldD/CafA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,389,811	0	C	.	97.1%	99.1 / ‑3.1	34	intergenic (‑148/+4152)	tldD/cafA	TldD/CafA
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (2/31);  total (3/31)
Fisher's exact test for biased strand distribution p-value = 8.82e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCG  >  NC_000913/3389736‑3389831                                                                            |                     ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc                      <  1:130241/76‑1 (MQ=255) ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc                      <  1:2731204/76‑1 (MQ=255) ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc                      <  1:4643862/76‑1 (MQ=255) ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCTGATGc                      >  2:1650181/1‑76 (MQ=255)  cAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTGcg                     >  1:346526/1‑75 (MQ=255)   aGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcgg                    <  1:5211521/76‑3 (MQ=255)    gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCGCAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc                   <  1:709349/76‑4 (MQ=255)    gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc                   <  1:3082397/76‑4 (MQ=255)    gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATGCggg                   >  1:3891249/1‑76 (MQ=255)      cTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGt                <  2:1860482/76‑1 (MQ=255)       tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa               <  2:839671/76‑1 (MQ=255)       tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa               <  1:3160731/76‑1 (MQ=255)         cGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTaaa             <  2:32652/76‑1 (MQ=255)          ggTTATGTTCCGGTTTGTAGGCCTGATCAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc            <  2:3910360/76‑1 (MQ=11)          ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc            <  1:5801250/76‑1 (MQ=255)           gTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg           <  1:4869095/76‑1 (MQ=255)           gTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg           <  1:2483518/76‑1 (MQ=255)           gTTATGTTCCGGTGTGTAGTCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGACGTAAACg           <  1:2493329/76‑1 (MQ=11)           gTTATGTTCCGGTGTGTAGGCGTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg           <  2:5416041/76‑1 (MQ=11)            ttATGTTCCGGTTTGTAGCCCTGATAATACGCACAGCGTCGCATCCGGCACCGGCTGTCGGATG‑CGGCGTAAACGc          <  1:5743007/76‑1 (MQ=11)            gtATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGc          <  2:3069796/75‑1 (MQ=255)             tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc         <  2:4877413/76‑1 (MQ=255)             tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc         <  1:2110610/76‑1 (MQ=255)              gtGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCt        <  2:5791986/75‑1 (MQ=255)               tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCtt       <  1:4141297/76‑1 (MQ=255)               tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCtt       <  1:4485042/76‑1 (MQ=255)               tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGGGTAAACGccct       >  1:5146473/1‑74 (MQ=11)                gtgccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa      <  1:399174/73‑1 (MQ=11)                gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa      <  1:3526576/76‑1 (MQ=255)                gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa      <  2:3733069/76‑1 (MQ=255)                gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa      <  1:4852129/76‑1 (MQ=255)                gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGCGGAAAAGCCCTa      >  1:3376912/1‑76 (MQ=11)                gTTCCGGTTGGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa      <  1:5663715/76‑1 (MQ=11)                 ttCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTAt     <  1:3330614/76‑1 (MQ=255)                 ttCCGGTTTGCAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTAt     <  1:3090152/76‑1 (MQ=11)                  tCCGTTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc    <  1:2150614/76‑1 (MQ=11)                  tCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc    <  2:3240369/76‑1 (MQ=255)                   ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc   <  2:3677818/76‑1 (MQ=12)                   ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc   <  1:5450969/76‑1 (MQ=12)                   ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc   <  1:3783178/76‑1 (MQ=12)                   ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc   <  1:1248525/76‑1 (MQ=12)                    cGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATCCg  <  1:4059183/76‑1 (MQ=9)                                                                            |                     CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCG  >  NC_000913/3389736‑3389831

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑