Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,139,498	T→C	30.8%	V21V (GTA→GTG)	USA300HOU_RS10910 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,139,498	0	T	C	30.8%	11.3 / 6.8	13	V21V (GTA→GTG)	USA300HOU_RS10910	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (4/5);  new base C (2/2);  total (6/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTTAATACATTCTCATCTATAATCTTATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAATATGGTTTCATACC  >  USA300TCH1516_ALE/2139362‑2139600                                                                                                                                         |                                                                                                       cGGTTAATACATTCTCATCTATAATCTTATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATTGCACTTTGTGTTACAt                                                                                                    >  1:58129/1‑141 (MQ=255) cGGTTAATACATTCTCATCTATAATCTTATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACAt                                                                                                    >  1:100052/1‑141 (MQ=255)                             atcttTTTGTTCTTGTNTATATTGCTTGANGTGTGGCTTCTTTAATAACCTACACCCTGTCACATGTGCACTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACaaa                                                                        >  1:114420/1‑141 (MQ=255)                             atcttTTTGTTCTTGTATATATTGCTTGATGTGTGGCTTCTTTAATAACCTACACCCTGTCACATGTGCACTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACaaa                                                                        >  1:9094/1‑141 (MQ=255)                                           gTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTg                                                          <  2:28553/141‑1 (MQ=255)                                                     cTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAactc                                                <  1:5476/141‑1 (MQ=255)                                                     cTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAactc                                                <  2:43617/141‑1 (MQ=255)                                                                       cAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCAccccc                              <  2:112308/141‑1 (MQ=255)                                                                           aaCCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACaa                          <  2:100901/141‑1 (MQ=255)                                                                                acacGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTa                     >  1:73958/1‑141 (MQ=255)                                                                                        tCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAatat             >  2:43218/1‑141 (MQ=255)                                                                                                   cTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACAAAACGCGCTTGCTTTGCCGTTAACTCACTCATTCTATCACCTCCACAATTTTATCTAATAAGGTTTCATAcc  <  2:114420/141‑1 (MQ=255)                                                                                                   cTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACAAAACGCGCTTGCTTTGCCGTTAACTCACTCATTCTATCACCTCCACAATTTTATCTAATAAGGTTTCATAcc  <  2:9094/141‑1 (MQ=255)                                                                                                                                         |                                                                                                       CGGTTAATACATTCTCATCTATAATCTTATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAATATGGTTTCATACC  >  USA300TCH1516_ALE/2139362‑2139600

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑