Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,677,695	C→T	38.4%	intergenic (‑145/+4)	ndk ← / ← pbpC	multifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase/fused transglycosylase and transpeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,677,695	0	C	T	38.4%	26.2 / 31.2	52	intergenic (‑145/+4)	ndk/pbpC	multifunctional nucleoside diphosphate kinase, apyrimidinic endonuclease, and 3'‑phosphodiesterase/fused transglycosylase and transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (26/6);  new base T (9/11);  total (35/17)
Fisher's exact test for biased strand distribution p-value = 1.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

TTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCACTGTCGCG  >  minE/1677636‑1677726                                                            |                                ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:2631369/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:998326/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:924977/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:89549/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:591352/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:578824/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:484968/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:2611400/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:2608655/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:2571313/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:2361510/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:1739876/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:1516320/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:114106/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:1244947/1‑69 (MQ=255) ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:1347888/1‑69 (MQ=255) ttGATCAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTg                        >  1:1768997/1‑69 (MQ=255)   gatgaAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGc                       >  1:2911595/1‑68 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTg                        >  1:2634608/1‑66 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCa                      >  1:3067123/1‑68 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:1129687/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:877961/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:738721/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:455723/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:3040194/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:2708636/1‑69 (MQ=255)    atgaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCAt                     >  1:1947377/1‑69 (MQ=255)      gaAGGTAAGATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:1304734/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAATAATCAGGGACAAAATAGACTATTGCATg                    <  1:1373284/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:2477835/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:519358/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:2270984/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:1442507/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:1041968/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:2385201/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:1396696/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:1170142/68‑1 (MQ=255)      gaAGGTAACATTTTTTTAAAATAAACCCAGTTTAAGCAACAATCAGGGACAAAATAGACTATTGCATg                    <  1:2712709/68‑1 (MQ=255)             aCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAAttt            >  1:289673/1‑69 (MQ=255)             aCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAAttt            >  1:319035/1‑69 (MQ=255)             aCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAAttt            >  1:1729967/1‑69 (MQ=255)             aCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAAtt             >  1:504789/1‑68 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTc           <  1:3331267/68‑1 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTc           <  1:2064139/68‑1 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTc           <  1:3123394/68‑1 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTc           <  1:2766049/68‑1 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCa          >  1:2146993/1‑69 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCa          >  1:2747902/1‑69 (MQ=255)               aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTAATGCATGACAAATTTc           <  1:1362472/68‑1 (MQ=255)                tttttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCAc         >  1:2076212/1‑69 (MQ=255)                tttttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCAc         >  1:2811241/1‑69 (MQ=255)                        aaataaaatGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCACTGTcgcg  <  1:656741/68‑1 (MQ=255)                                                            |                                TTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTCACTGTCGCG  >  minE/1677636‑1677726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑