Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,866,110	T→A	intergenic (‑20/+160)	rpoS ← / ← nlpD	RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,866,110	0	T	A	100.0%	175.9 / NA	55	intergenic (‑20/+160)	rpoS/nlpD	RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (21/34);  total (21/34)

TGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATT  >  W3110S.gb/2866057‑2866174                                                      |                                                                 tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                              >  1:3805408/1‑58 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:869349/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:2755282/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:687105/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:2859918/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:2294547/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:3663494/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:2293556/70‑1 (MQ=255) tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt                                                  <  1:3454878/70‑1 (MQ=255)              tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt                                    >  1:2858677/1‑71 (MQ=255)              tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt                                    >  1:3999118/1‑71 (MQ=255)              tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt                                    >  1:3308115/1‑71 (MQ=255)                aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                                   <  1:1681079/70‑1 (MQ=255)                aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                                   <  1:1772993/70‑1 (MQ=255)                aCAATTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                                   <  1:2646334/70‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:3402347/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:3690281/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:1477283/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:3122566/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:136739/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:806169/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:840275/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:2595494/40‑1 (MQ=255)                 cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt                                                                <  1:2606140/40‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:343679/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:3514432/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:271648/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:2532956/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:1242762/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:2024846/71‑1 (MQ=255)                               ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:2424437/71‑1 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   >  1:1963087/1‑70 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   <  1:1162317/70‑1 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   >  1:140968/1‑70 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   >  1:3955610/1‑70 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   >  1:2161501/1‑70 (MQ=255)                                cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                   >  1:3373446/1‑70 (MQ=255)                                            aCTGGGTTCCAATTCTCCTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCt       <  1:2394065/70‑1 (MQ=255)                                            aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc              <  1:2062348/63‑1 (MQ=255)                                            aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc              <  1:3106138/63‑1 (MQ=255)                                            aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc              <  1:1768732/63‑1 (MQ=255)                                            aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc              <  1:2468587/63‑1 (MQ=255)                                            aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc              <  1:2514895/63‑1 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt               >  1:1201963/1‑60 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:1086288/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:285260/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:745948/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:744624/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:657443/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:2924515/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:1899556/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:1904823/1‑63 (MQ=255)                                              tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg            >  1:3130838/1‑63 (MQ=255)                                              tGGCTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa                 >  1:62100/1‑58 (MQ=255)                                                ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAtt  >  1:1077573/1‑71 (MQ=255)                                                      |                                                                 TGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATT  >  W3110S.gb/2866057‑2866174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑