Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	12,357	T→C	T65T (ACT→ACC)	dnaK →	chaperone protein DnaK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	12,357	0	T	C	95.2%	52.7 / ‑6.5	21	T65T (ACT→ACC)	dnaK	chaperone protein DnaK
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (13/7);  total (13/8)
Fisher's exact test for biased strand distribution p-value = 3.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

CCGAATATATAGTGGAGACGTTTAGATGGGTAAAATAATTGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGCGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTAG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CTCTGTTTGCGATTAAACGCCTGATTGGTCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATTTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCTGAAGATTACCTGGGTGAACCGGTAACTGAAGCTGTTATCACCGTACCGGCATACTTTAAC  >  NC_000913/12138‑12603                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                       ccGAATAAATAGTGGAGACGTGTAGATGGGTAAAATAATTGGTATCGTCCTTGGTACTACCAACTCTTGTGGAGCGATTATGGATGGCACCACTCCTCGTGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGGCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAACCGCCTGATTGgccgcc                                                                                                                                                                                                                         <  2:132076/251‑1 (MQ=255)              ggAGACGTTTAGATGGGTAAAATAATTGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGTGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACg                                                                                                                                                                                                             <  1:179098/250‑1 (MQ=255)               gagaCGTTTAGATGGGCAAAATAAATGGTATCGCCCTGGGTACTACCACCTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGTGTGATGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGACTATACCCAGGATGGTGAAACTCTAG‑TTGGTCAGACGGCTAAACGTCCGGCAGTGACGAACCAG‑AAAACAACCCTGTTTGCGATTCAACGCCTGATTGGACACCGCTTCCAGGACga                                                                                                                                                                                                            >  2:219083/1‑250 (MQ=255)                            gggTAAAATAATTGGTATAGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGTGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTg                                                                                                                                                                                              >  1:67164/1‑251 (MQ=255)                                       ttGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGTGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTATACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGCTTGGCCGCCGATTCCAGGACGGATAAGTActggt                                                                                                                                                                                                >  2:5340/1‑234 (MQ=255)                                       ttGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGTGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCg                                                                                                                                                                                                <  1:5340/238‑1 (MQ=255)                                                              caCTCGTGTGTAGCGATTATGGATTGCAACACTTCTCGTGTGCTGGAGAACGTCGTAGGCGATCGAATCTTGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCTGCTAAACGTCAGGCAGTGACGAACCCGCAAATCA‑CCCTGTTTGCTATTAAATGCCTGATTGGCAGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCCTCATGCCGTTCAAAATTATtgctgc                                                                                                                                                            <  1:277433/250‑1 (MQ=255)                                                                                  ggatggCACCACTCCTCGCGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTAG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CTCTGTTTGCGATTAAACGCCTGATTGGTCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATgg                                                                                                                                         <  1:48756/250‑1 (MQ=255)                                                                                                    tgTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGAt                                                                                                                                                        >  1:381721/2‑217 (MQ=255)                                                                                                    tgTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGAt                                                                                                                                                        <  2:381721/216‑1 (MQ=255)                                                                                                                  ccGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAACATTATTGCTGCTGATAACGGCGACGCATGGGCCGACGTTAAAGTCCAGAAAATGGCAccgccg                                                                                                        >  2:134485/1‑251 (MQ=255)                                                                                                                              gCACCACGCCTTCTATAATTGCCTATACCCAGGATGGTGAAACTCTGA‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGAAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTTCAGCGTGATGTTTCCATCATGCCGTTCAAACTTATTGCTGCTGAGAACGGAGACGCATGGTTCGCACTTAAAGGCCAGACAATGGCACCGCGGCAAATCTctgct                                                                                            >  2:118430/1‑251 (MQ=255)                                                                                                                                    cGCCTTCTATCATTGCATATACCCAGGATGGTGTAACTCTGG‑TTGGTCAGCAGGCTAAACGTCAGGCAGTGACGAACCCGAAAAACA‑CCATGTTTGCGATTCACCGCATGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATAATGCCGTTCAAAATTATTGCTGCTGCTAACGGCGACGCATGGGTCGACGTTAACGGCCAGAAAATGGCACCGCCGCAGATCTCTGCTGAAg                                                                                        >  1:375766/1‑249 (MQ=255)                                                                                                                                                            aGGATGGTGAAAC‑CTGGGTTGGTCAGCCGGCAAAACGTCAGGCATGGACGACCCCGCAAAACC‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCACCTTGCCGTACAAAATTATGGCTGCTGATAACGGCGACGCAGGGGTCGAAGTTAAAGGCAAGAAAATGGCACCGCCGCAGATCTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCt                                                              <  1:168419/251‑1 (MQ=255)                                                                                                                                                               aTGGAGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATATCTGCTGAAGAGCTGAAAAAAATGAAGAAAACCGCTGa                                                            >  1:151618/1‑250 (MQ=255)                                                                                                                                                                  gTGAAACTCTGG‑TTGGTCAGCCGGCTAAACGTAAGGAAGTGACGAACCCGCAACACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAAAAGAAAAGCCTGACGTTTCCATCATGCAGTTAACAATTATTGCTGCTGATAACGGAGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCTGCAGATCTCTGATGAAGTGCGGAAAAAAATGAAGAAAACCGCTGa                                                            >  1:368451/1‑247 (MQ=255)                                                                                                                                                                          ctgg‑TTGGTCAGCCGGCTAAACGACAGGCAGTGACGAACCCGCCAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGACAATGGCACCGCCGCAGATCTCTTCTGAAGTGCTGAAAAAAATGAATAAACCCGCTGAAGATTGCCTggg                                                >  2:206106/4‑251 (MQ=255)                                                                                                                                                                                                        aGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATATCTGCTGAAGTGCTGaaaaaac                                                                            >  2:292988/1‑193 (MQ=255)                                                                                                                                                                                                        aGTGACGAACCCGCAAAACA‑CCCTGTTTGCGATAAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATCTCTGCTGAAGTGCTGaaaaaaa                                                                            <  1:292988/194‑1 (MQ=255)                                                                                                                                                                                                             cGAACCCGCAAAACA‑CCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATCTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCTGAAGATTACCTGGGTGAACCGGTAACTGAAGCTGTTATCACCGTACCg              >  1:294849/1‑251 (MQ=255)                                                                                                                                                                                                                         aca‑cCCTGTTTGCGATTAAACGCCTGATTGGCCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATCTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCTGAAGATTACCTGGGTGAACCGGTAACTGAAGCTGTTATCACCGTACCGGCATACTTTAAc  >  1:146665/1‑251 (MQ=255)                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                       CCGAATATATAGTGGAGACGTTTAGATGGGTAAAATAATTGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTATGGATGGCACCACTCCTCGCGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTATACCCAGGATGGTGAAACTCTAG‑TTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACA‑CTCTGTTTGCGATTAAACGCCTGATTGGTCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCATGCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCGCCGCAGATTTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCTGAAGATTACCTGGGTGAACCGGTAACTGAAGCTGTTATCACCGTACCGGCATACTTTAAC  >  NC_000913/12138‑12603

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑