Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,097,480	Δ1 bp	100%	coding (1/963 nt)	pfkA →	6‑phosphofructokinase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,097,480	0	A	.	100.0%	90.1 / NA	20	coding (1/963 nt)	pfkA	6‑phosphofructokinase I
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (12/8);  total (12/8)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCTGACCTGAATCAATTCAGCAGGAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTCATGATTAAGAAAATCGGTGTGTTGACAAGCGGCGGTGATGCGCCAGGCATGAACGCCGCAATTCGCGGGGTTGTTCGTTCTGCGCTGACAGAAGGTCTGGAAGTAATGGGTATTTATGACGGCTATCTGGGTCTGTATGAAGACC  >  CP009273/4097354‑4097624                                                                                                                               |                                                                                                                                                 cctgacctgaATCAATTCAGCAGGAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcc                                                                                                                          <  1:192227‑M1/150‑20 (MQ=255)    gacctgaATCAATTCAGCAGGAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctt                                                                                                                        >  2:4757‑M1/1‑128 (MQ=255)                 tCAGCAGGAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccga                                                                                                          >  1:7420‑M1/1‑115 (MQ=255)                       ggAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatga                                                                                                       >  2:31071‑M1/1‑109 (MQ=255)                            tGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagc                                                                                                >  2:709‑M1/1‑104 (MQ=255)                                    ataCTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgc                                                                                        <  2:26267‑M1/149‑54 (MQ=255)                                               acaTTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttc                                                                            >  1:64450‑M1/1‑85 (MQ=255)                                                         gATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcagg                                                                  >  2:118035‑M1/1‑75 (MQ=255)                                                                  gATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatg                                                          <  2:7420‑M1/149‑84 (MQ=255)                                                                           gaagaCTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaa                                                <  1:118035‑M1/150‑94 (MQ=255)                                                                            aagaCTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgtaat                                               >  1:77807‑M1/1‑56 (MQ=255)                                                                                   ccGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattg                                         >  1:25152‑M1/1‑49 (MQ=255)                                                                                         aCAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcgggcctacatgaattctgcaatttattgaatttg                                   >  2:86363‑M1/1‑43 (MQ=255)                                                                                                tCATTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaactt                            <  1:709‑M1/149‑114 (MQ=255)                                                                                                  aTTTTGCATTCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaactttt                          <  1:31071‑M1/149‑116 (MQ=255)                                                                                                          ttCCAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaacttttgtaggccgg                 <  1:158751‑M1/150‑125 (MQ=255)                                                                                                            ccAAAGTTCAGAGGTAGTC‑TGATTtcggaaaaaggcagagtcctttaccctgaaaccgatgacagaagcaaaaatggctgatgcgcttcacttagcaggcctacatgaattctgcaatttattgaatttgcaaacatttgtaggccgga                <  2:99606‑M1/149‑126 (MQ=255)                                                                                                                     agagGTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaacttttgtaggccggataaggcgttc      >  1:183553‑M1/1‑15 (MQ=255)                                                                                                                         gTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaacttttgtaggccggataaggcgttcgcgc  >  2:182312‑M1/1‑11 (MQ=255)                                                                                                                         gTAGTC‑TGATTtcggaaaaaggcagattcctttaccctgaaaccgatgacagaagcaaaaatgcctgatgcgcttcgcttatcaggcctacatgaattctgcaatttattgaatttgcaaacttttgtaggccggataaggcgttcgcgc  >  2:15444‑M1/1‑11 (MQ=255)                                                                                                                               |                                                                                                                                                 CCTGACCTGAATCAATTCAGCAGGAAGTGATTGTTATACTATTTGCACATTCGTTGGATCACTTCGATGTGCAAGAAGACTTCCGGCAACAGATTTCATTTTGCATTCCAAAGTTCAGAGGTAGTCATGATTAAGAAAATCGGTGTGTTGACAAGCGGCGGTGATGCGCCAGGCATGAACGCCGCAATTCGCGGGGTTGTTCGTTCTGCGCTGACAGAAGGTCTGGAAGTAATGGGTATTTATGACGGCTATCTGGGTCTGTATGAAGACC  >  CP009273/4097354‑4097624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑