Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,257,869	C→T	A48T (GCG→ACG)	cyuP ←	cysteine detoxification protein CyuP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,257,869	0	C	T	94.4%	46.4 / ‑6.0	18	A48T (GCG→ACG)	cyuP	cysteine detoxification protein CyuP
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (12/5);  total (12/6)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACATCCAAATCACCAGCATTACGAAATAGAGCGCACCTAACAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGCCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTACGTTTTTGCAGGCGAGTTATTAGAAT  >  NC_000913/3257626‑3258106                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              cGAACATCCAAATCACCAGCATTACGAAATAGAGCGCACCTAACAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCg                                                                                                                                                                                                                                        >  1:6498/1‑251 (MQ=255)                               agagCGCACCCAACAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAACAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGt                                                                                                                                                                                                           >  2:267567/1‑250 (MQ=255)                                 agCGCACCTAACAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑AAAAAATACCCACAATCCCATCAAACCGACCTGCACAGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACt                                                                                                                                                                                                        >  2:70668/1‑251 (MQ=255)                                       ccTAACAGGATGCCCCAGTTTTTACCTAAATAAACGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCAGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTCCTGTCGa                                                                                                                                                                                                   >  1:121973/1‑250 (MQ=255)                                           aCAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACGCATAATCACCCAGCCGGTGTCAGTACTGTCGAAttta                                                                                                                                                                                              <  1:17110/251‑2 (MQ=255)                                                            ttACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTc                                                                                                                                                                             >  2:230898/1‑251 (MQ=255)                                                               ccTAAATAACCGCTAATGACGCTCGGGCAATCTTTACATTCTGGAGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCAAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGct                                                                                                                                                                          >  1:21198/1‑251 (MQ=255)                                                                                                         ggTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCCCCGGGAGAAAAACAATCCCCTCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGAGCGCTTCTCGCCCCTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTg                                                                                                                                 <  1:157375/250‑1 (MQ=255)                                                                                                                   ccAGCGTATTAATGAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCACGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTAGCCACTCGCTCTCACTCATTCCAGCACGACCAGCCGGGGTCGACGCGTCTGCAATGACgact                                                                                                                      >  2:7530/1‑248 (MQ=255)                                                                                                                                    aaTCGCTGAAACAAAAACATTGCCGGGTAACCAATACCCGAGGA‑AGACAAAAATACCCACAACCCCATCAACCCGACCTGCCCCGGAAGAAAAACAACCCCCGCGCCAATCGTCAACCCGATACTCATAAGCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACGCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTc                                                                                                     <  2:200377/251‑1 (MQ=255)                                                                                                                                                      aTTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCAGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGCTGCAATTTCCATCATTTCTCGCTCAat                                                                                   >  1:46477/1‑251 (MQ=255)                                                                                                                                                              gTAACCAATCACCAATGAGAG‑CAAAAAAACCCACAATCCCCTCAACCCGACCTGCACCGGGAAAAAACCAATCCCCGCGCCAAGCGTCATCCCGATACTCATAATCCCCCAGCCTGTGACAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGTGGTCGAAGCGTCTGCAATGACTCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTa                                                                           <  2:118643/251‑1 (MQ=255)                                                                                                                                                              ataacaaagccccGAAGAGAG‑CAAAAATACCCAAAAACCAATCAAACCAACCTGCCCCGGGAAAAAACCAAACCCCGCGACAATCGTCACCCCGATACTCATAATCCCCCAGCCTGTTCCAGTACGGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCTGGGTCGAAGCGTCTGCAATGACTCCTTTATTCGATGCAATTTCCAGAATTTCTCGCTCAATATATTGTa                                                                           <  2:92845/240‑1 (MQ=255)                                                                                                                                                                                                               gACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTAc                           >  1:179319/1‑251 (MQ=255)                                                                                                                                                                                                                       ccGGGAGAAAAACAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTACGTTTTTGc                   >  2:230741/1‑251 (MQ=255)                                                                                                                                                                                                                             aaaaaaCAACCCCCCCGCAAATCGCCATCCCGATACTAAAAAACCCCCGGCCGGTGTCAGTACTGTCGAATTGGATCGCTTCTCGCCCCTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTACGTTTTTGCAGGCGa             <  2:224816/250‑1 (MQ=255)                                                                                                                                                                                                                                  aCAATCCCCGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTCCTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCACTATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTACGTTTTTGCAGGCGAGttat        >  1:124779/1‑251 (MQ=255)                                                                                                                                                                                                                                         ccGCGCCAATCGTCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGCTATGCGGTCTACGTTTTTGCAGGCGAGTTATTAGAAt  >  1:18462/1‑250 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              CGAACATCCAAATCACCAGCATTACGAAATAGAGCGCACCTAACAGGATGCCCCAGTTTTTACCTAAATAACCGCTAATGACGCTCGGGTAATCTTTACATTCTGGTGATTCTGCCAGCGTATTAATAAACAATCGCTGAAACAGATACATTGCCGGGTAACCAATCACCGATGAGAG‑CAAAAATACCCACAATCCCATCAAACCGACCTGCACCGGGAGAAAAACAATCCCCGCGCCAATCGCCATCCCGATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGCACGACCCGCCGGGGTCGAAGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTCAATATTTTGTAGGGCTTATTATTTTTTTCCGAGCCGCATCAAGGCGATATGCGGTCTACGTTTTTGCAGGCGAGTTATTAGAAT  >  NC_000913/3257626‑3258106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑