Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,583,969	0	G	A	71.4%	20.4 / 13.8	21	W98* (TGG→TAG)	insB6	IS1 family protein InsB
Reads supporting (aligned to +/- strand):  ref base G (3/3);  new base A (4/11);  total (7/14)
Fisher's exact test for biased strand distribution p-value = 3.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.44e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGCGCACGTATTCGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGA  >  NC_000913/3583889‑3584218                                                                                 |                                                                                                                                                                                                                                                           tgngaaCGTATTCGGTGAACGCACGATGGCGATGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGAGGACGGATGGCTGGCCGCTGTATGAATCCCACCAGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAAGCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGAc                                                                                  <  2:1126603/245‑1 (MQ=255)                                                          gTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGTCAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTGGGAGTCATTACCg                        <  2:1233619/251‑1 (MQ=11)                                                          gTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCg                        <  1:476068/251‑1 (MQ=11)                                                          gTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCg                        >  1:789441/1‑251 (MQ=11)                                                           tCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCg                        >  2:765999/1‑250 (MQ=11)                                                            cACCCTTTGACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGTACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGa                       <  1:102995/250‑1 (MQ=11)                                                            cACCCTTTGACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAc                      >  2:1061921/1‑251 (MQ=14)                                                             aCCCTTTGACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAc                      >  2:399750/1‑250 (MQ=14)                                                               ccTTTGACGTGGTGGTATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAATT‑CGCTGTCGTTCTCAAAATCGGGGGAGCTGCATGACAAAGTCATCGGTCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAtt                   <  1:237340/251‑1 (MQ=255)                                                               ccTTTGACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTAAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCGCCTGGCAGGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAtt                   <  1:1231210/251‑1 (MQ=12)                                                                cttggACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCGGCACGTAAACAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATGACCGACAt                    <  2:449991/245‑1 (MQ=255)                                                                   tGACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAAGCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCTATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACGAGCAATAAGTTGGAGTCATTACCGACATTaaa                <  1:896162/250‑1 (MQ=255)                                                                    gACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaaaa               <  2:917233/250‑1 (MQ=21)                                                                    gACGTGGTGATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAg              <  1:1123590/251‑1 (MQ=21)                                                                    gACGTGGTGATATAGATGACGGAGGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGATTCATTACCGACATTaaaa               <  2:1069308/250‑1 (MQ=21)                                                                       gtggtgATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTa            >  2:1037196/1‑250 (MQ=25)                                                                       gtggtgATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTa            >  1:305499/1‑250 (MQ=25)                                                                        gggtgATATAGATGACGGATGGCTGGCTGCTGTATGAATCCCGCCTGAAGGGAAATCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAGAGTAAc          <  2:125001/250‑1 (MQ=255)                                                                            gATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGATTCATTACCGACATTAAAAGTAACtttt      <  1:1092954/251‑1 (MQ=255)                                                                            gATATAGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtttt      <  2:801903/251‑1 (MQ=38)                                                                                tGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGCCAGGCCTGGG‑CGGGAGTTCGCGGTGGTTCTCAAAATCGGGGGGGCTCCAGGCCAAGGTAATGGGGCATTATTGGAACATAAACCATTACCAAAAGGTTGGAG‑CATTaaagatggaaagggcgtggggggggg  >  2:854345/1‑225 (MQ=255)                                                                                 |                                                                                                                                                                                                                                                           TGCGCACGTATTCGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGT‑CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGA  >  NC_000913/3583889‑3584218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑