Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,158,853	Δ1 bp	coding (138/825 nt)	thiK →	thiamine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,158,850	0	T	.	96.0%	98.0 / ‑4.0	25	coding (135/825 nt)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base . (5/19);  minor base G (1/0);  total (6/19)
Fisher's exact test for biased strand distribution p-value = 2.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGT  >  NZ_CP009273/1158731‑1158978                                                                                                                        |                                                                                                                                 aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCa                                                                                                              <  2:977759/139‑1 (MQ=255) aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCa                                                                                                              <  1:420379/139‑1 (MQ=255) aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCa                                                                                                              <  1:162729/139‑1 (MQ=255) aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCa                                                                                                              <  1:221263/139‑1 (MQ=255)  ataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGGTTTTTCATTTTACATAATGGACCGCG‑GTTGTTGTGTGGCAGCCGccc                                                                                                             >  2:1283708/1‑137 (MQ=255)             aCGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGGTTTTTTTTTAAAATCACGGGCAGCGGTTT‑TTGTGCGTCGGCCCCCCGGTCCTGATgc                                                                                                  >  2:1233104/1‑139 (MQ=255)                        aTTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCcg                                                                                       <  1:624929/139‑1 (MQ=255)                                   gcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTgcgc                                                                            <  1:251140/139‑1 (MQ=255)                                          cccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAt                                                                      <  2:306069/138‑1 (MQ=255)                                          cccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAt                                                                      <  2:1002062/138‑1 (MQ=255)                                          cccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTAt                                                                      <  2:1100515/138‑1 (MQ=255)                                           ccGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCg                                                                    <  1:1236722/139‑1 (MQ=255)                                                 tATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCATTTAACATCAGGGGCAGCG‑GTTGTTGTGGGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGGTCTTGTGGCAGGATCgggggtt                                                              >  1:306069/1‑135 (MQ=255)                                                           tCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGTTTTTTTCTTTTACATCAAGGCCCGCG‑GTTGTTGTGGGGCCGCCGCCCCGTCCTGATGCGCCGCAGGCCGCGGTTTTTCGCCCGTATCGGGCGTTTTTACAACTa                                                    >  2:370716/1‑139 (MQ=255)                                                                acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                               <  1:370716/139‑1 (MQ=255)                                                                acgTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgc                                               <  1:1045200/139‑1 (MQ=255)                                                                             ggCTTAGTGGCGGGAGGTTTTTCCTTTTACATCAAGGCCCGCG‑GTTGTTGTTCGTCAGCCGCCCGATCCTTATGCGCCGCCGTCCGCGGTCTTGCGCCAGTATCGGGGTTTTTTACAACTACCCCCATGCATTGCACCg                                  >  1:797913/1‑139 (MQ=255)                                                                                          gAGTTTTCTCATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTtat                     <  1:1110279/139‑1 (MQ=255)                                                                                                tctcATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATAtctc                <  2:197717/138‑1 (MQ=255)                                                                                                tctcATTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATAtctc                <  2:214547/138‑1 (MQ=255)                                                                                                    aTTGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGa           <  2:162828/139‑1 (MQ=255)                                                                                                      tGAACATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACt         >  1:645255/1‑139 (MQ=255)                                                                                                         aCATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGa      <  2:31819/139‑1 (MQ=255)                                                                                                         aCATCAGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGa      <  2:741101/139‑1 (MQ=255)                                                                                                              aGGGCCAGCG‑TTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGt  <  1:237425/138‑1 (MQ=255)                                                                                                                        |                                                                                                                                 AATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGT  >  NZ_CP009273/1158731‑1158978

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑