Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	1,123,238	0	C	A	60.0%	‑4.7 / 13.0	31	intergenic (‑240/+64)	gcvH_1/CJ019_01062	Glycine cleavage system H protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (5/7);  new base A (18/0);  total (24/7)
Fisher's exact test for biased strand distribution p-value = 3.89e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CAATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCT  >  ACB143/1123104‑1123374                                                                                                                                         |                                                                                                                                           cAATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAACCCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGc                                                                                                                                          >  6:51584/1‑137 (MQ=255)            gTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑AAGACGTAgg                                                                                                                              >  7:189181/1‑136 (MQ=255)              aaaTTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑a                                                                                                                           >  1:26377/1‑137 (MQ=255)                                  ttttttGTGTTTAATTATATCTTTACGGGGGCCGCGGACAGTAAAAGGGTTTGACCA‑CAAACCCATTGTGCACGGACGGCGCGGTGGCTGTTTTTGGTTTT‑CCAA‑ACCACGTCCCA‑AAAACGATACATGTGGTGCCt                                                                                                       <  6:174703/137‑1 (MQ=255)                                          gtgGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGCTACATGTGGTGCCTGGACTGGc                                                                                               >  5:85891/1‑137 (MQ=255)                                           tgcaaTTATAGCGTTCCCGGGGCCTCTCAGAGTAAAAGGGTTTCCCCAGAAAACCG‑TTGTGCACCGACGGCGACGCGGCTGGGAAGCGTTTG‑CGCA‑ACGCCGTAGCT‑AAACCGATACATGTGGTGCCTGGACTGGCg                                                                                              <  8:303483/134‑1 (MQ=255)                                             gAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAg                                                                                            >  5:137625/1‑137 (MQ=255)                                              aaTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGAAACATGTGGTGGCTGGACTggggggg                                                                                           >  3:83904/1‑132 (MQ=255)                                              aaTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑AAGACGTTGAG‑AAAACGATACATTTGGTGGCGTGTCTGGCGAgg                                                                                           >  1:93380/1‑137 (MQ=255)                                               aTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑TCGACGGTGCGCAAACCGATA‑AAGTTGTGGCTGGGCTGGCGGGGt                                                                                          >  6:35987/1‑137 (MQ=255)                                               aTGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGGAGCG‑AAAAAGATACATGTGGTGGCTGGACTGGCGAGGt                                                                                          >  1:205728/1‑137 (MQ=255)                                                      cGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAAtt                                                                                   >  8:89423/1‑136 (MQ=255)                                                      cGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCTAACCAC‑TATCG‑AAAAACAAAAATGTGGTGGCTTGCCAGGCGCTGTGGCAAtt                                                                                   >  6:214873/1‑136 (MQ=255)                                                        ttACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGc                                                                                 >  7:148057/1‑137 (MQ=255)                                                        ttACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGGAGCG‑AAAAAGATACATGTGGTGCCTGGGCTGGCGGGGTGCCAATggg                                                                                 >  3:272188/1‑136 (MQ=255)                                                         accAGGGGCCTCTCCGGGTAAAAGGGTTTCTGAATCAAACCG‑TTGTGCCCCTAGGGCTAGGTGGCTTTGTTGGGTTTT‑CGCT‑CCGAGGTCGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGcc                                                                                <  2:53603/135‑1 (MQ=255)                                                           cAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCG‑ACGCCCTAGCC‑TAAACCATACATGGGGTGCCGGGTCTGGCGTGGGGGCCATGGccgg                                                                              >  1:287647/1‑135 (MQ=255)                                                                    ctGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTAGGGT‑AC‑ACGTTGCC‑GAAACCATACATTTGGTGCCGGGACATGCGGGGTGCCAATGGGCTTCGGGCAtct                                                                     >  8:36069/1‑137 (MQ=255)                                                                    ctGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCAtct                                                                     >  7:202662/1‑137 (MQ=255)                                                                         accaaaaGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACTTAGCT‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACtt                                                                <  5:162433/134‑1 (MQ=255)                                                                            aaaaGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGATACCTGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCCTCTCACtttaa                                                             >  7:263680/1‑135 (MQ=255)                                                                                 ggTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGGAGCG‑AAAACGATACATGTGGTGGCTGGACTGGCGAGGTTCCCATGGCCTTAGGGCATCTCACTTTCAGCAga                                                        >  7:309799/1‑137 (MQ=255)                                                                                               aCCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGaaaa                                          >  2:28817/1‑137 (MQ=255)                                                                                                        gCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTATCG‑AAAAAGCTAAATGTGGTGGCGGGACTGGCGATGTGGCAATTGCCTTCGGTCATCTCACTTTCAGCAGATGATCCCGCGAAAACGCCCCgg                                  >  4:117297/1‑137 (MQ=255)                                                                                                         cACCGACGGCTCGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACTTAGCT‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGgc                                 <  5:328025/137‑1 (MQ=255)                                                                                                               cGGCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTAGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCg                           >  6:314216/1‑137 (MQ=255)                                                                                                                 gCGAGGAGGCTGTGTATCGTTTT‑AGCT‑ACGACGTAGCG‑AAAACGATAAATGTGGTGGCTTGACTGGCGAGGTGCCAATTGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCCCCCGCGCCGCggg                         >  8:83178/1‑137 (MQ=255)                                                                                                                 gCGAGGAGGCTGTGTATCGTTTT‑AGCG‑ACGCCGTTGCG‑AAAACGATACATGTGGTGGCGGGCCAGGCGAGGTGCCAATGGCCTTAGGTCATATGACTTTAAGCAGATGATACAGCGAAAACCCCCCGGCGCCTCggg                         >  8:142760/1‑137 (MQ=255)                                                                                                                        ggCTGTGTATCTTTTT‑CGAT‑ACGACGTAGCT‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAATGCGCCGGCGCCTCGGGCAACCAg                  <  8:202662/137‑1 (MQ=255)                                                                                                                              ttagcGTTTT‑CGCT‑ACGACGTAGCT‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGagcag            <  8:263680/133‑1 (MQ=255)                                                                                                                                aTCGTTTT‑CGCG‑ACGACGGAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCCGCAGATGATCCAGCGAACACGCGCCGGCGCCTCGGGCAACCCGGAgccgca          >  6:333303/1‑137 (MQ=255)                                                                                                                                         cGCT‑ACGACTTAGCT‑AAAACGATACATGTGGTGCCTGGACTAGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCt  <  5:314216/137‑1 (MQ=255)                                                                                                                                         |                                                                                                                                           CAATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGAGCATCAAACCC‑TTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTT‑CGCT‑ACGACGTAGCG‑AAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGTCATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCT  >  ACB143/1123104‑1123374

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑