Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	4,964,454	0	C	T	44.0%	1.8 / 28.8	25	D302N (GAC→AAC)	fleQ	Transcriptional regulator FleQ
Reads supporting (aligned to +/- strand):  ref base C (5/9);  new base T (5/6);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 6.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CATGATCGCCATGCGCTCGACCAGGTTGGCCAGCTCGCGTACGTTGCCCGGCCAGCCGTGACGACACAGCGACATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTT  >  AE015451/4964233‑4964646                                                                                                                                                                                                                              |                                                                                                                                                                                                 cATGATCGCCATGCGCTCGACCAGGTTGGCCAGCTCGCGTACGTTGCCCGGCCAGCCGTGACGACACAGCGACATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGcc                                                                                                                                                                                   >  1:351179/1‑237 (MQ=255)    gATCGCCATGCGCTCGACCAGGTTGGCCAGCTCGCGTACGTTGCCCGGCCAGCGGGGACGACACAGCGACATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGACGGTAGTACAGGTCt                                                                                                                                                                                                 <  2:239592/220‑1 (MQ=255)                                     gcgTACGTTGCCCGGCCAGCCGTGACGACACAGCGACATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGc                                                                                                                                               >  1:379699/1‑237 (MQ=255)                                                                         cATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATgg                                                                                                                                                                     >  2:5941/1‑179 (MQ=255)                                                                              tCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCg                                                                                                                                                                <  1:5941/179‑1 (MQ=255)                                                                                              gCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCt                                                                                                               <  1:55730/212‑1 (MQ=255)                                                                                              gCGAATGGAACCGCGCTTCTCGTGCTCCATGCGAGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACATTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGc                                                                                                                                            <  2:12627/183‑1 (MQ=255)                                                                                                    ggAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCAcgc                                                                                                >  1:291368/1‑221 (MQ=255)                                                                                                          gngcTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAg                                                                                                                                                                                        <  2:100013/127‑1 (MQ=255)                                                                                                                   gTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAg                                                                                                                                                                                        >  1:110403/1‑118 (MQ=255)                                                                                                                   gTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAg                                                                                                                                                                                        <  2:110402/118‑1 (MQ=255)                                                                                                                                  aaTCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCa                                                   >  1:436450/1‑236 (MQ=255)                                                                                                                                               atcaGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCg                                                                                                                                                <  2:254348/130‑1 (MQ=255)                                                                                                                                               atcaGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCg                                                                                                                                                >  1:254350/1‑130 (MQ=255)                                                                                                                                                     aaCGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCGTTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTACTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGc                                                                                                                        <  2:234902/148‑1 (MQ=255)                                                                                                                                                     aaCGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCt                                                                                                               >  1:373089/1‑157 (MQ=255)                                                                                                                                                     aaCGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCt                                                                                                               <  2:373087/157‑1 (MQ=255)                                                                                                                                                              tCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGtt                                                                                                                                                                   <  2:311033/96‑1 (MQ=255)                                                                                                                                                                ttCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAg                    <  1:439625/237‑1 (MQ=255)                                                                                                                                                                    aCCCGCTCACGCAGCGGCGCCAGTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCa                                                                                                                                              <  2:191063/111‑1 (MQ=255)                                                                                                                                                                           cACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACATGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTAc         >  1:178605/1‑237 (MQ=255)                                                                                                                                                                              gCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTtcg                         <  1:241546/218‑1 (MQ=255)                                                                                                                                                                                           ttCGATAGGGAACACGTTCAGGCGGTAGTGCAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCttg                                                                                                             <  1:62164/121‑1 (MQ=255)                                                                                                                                                                                           ttCGATAGGGAACACGTTCAGGCGGTAGTACAGGTTTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCttg                                                                                                             >  2:62163/1‑121 (MQ=255)                                                                                                                                                                                                             cAGGCGGTAGTACAGGTCTTCGCGGGAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGtt  <  1:152673/210‑1 (MQ=255)                                                                                                                                                                                                                              |                                                                                                                                                                                                 CATGATCGCCATGCGCTCGACCAGGTTGGCCAGCTCGCGTACGTTGCCCGGCCAGCCGTGACGACACAGCGACATGATCGAGGCGGAATTGAAGCGAATGGAACCGCGCTTCTCGTGCTCCATGCGCGAAATCAGCTCGTTCATCAGCAACGGGATGTCTTCCACCCGCTCACGCAGCGGCGCCATTTCGATAGGGAACACGTTCAGGCGGTAGTACAGGTCTTCGCGGAAGGTGCCGTCCTCGATCATGGTTTCGAGGTTCTTGTGCGTCGCAGCGATGATGCGCACGTCGATGCTTTGGGTCTTGTTGCTACCCACGCGCTCGAAGGTACGCTCCTGCAGCACACGCAGCAGCTTGACCTGCATCGGCAACGGCATGTCGCCGATTTCGTCGAGGAACAGGGTACCGCCGTT  >  AE015451/4964233‑4964646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑