Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,514,749	C→T	A351T (GCA→ACA)	rlmL ←	Ribosomal RNA large subunit methyltransferase L

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,514,749	0	C	T	100.0%	61.4 / NA	23	A351T (GCA→ACA)	rlmL	Ribosomal RNA large subunit methyltransferase L
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/8);  total (15/8)

ACTTAATTATTACTAATTTTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTT  >  USA300TCH1516_ALE/1514614‑1514880                                                                                                                                        |                                                                                                                                    aCTTAATTATTACTAATTTTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTa                                                                                                                                 >  1:175163/1‑140 (MQ=255)     aaTTATTACTAATTGTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGAt                                                                                                                             <  2:172680/140‑1 (MQ=255)            aCTAATTTTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATTCATTAAATAACTTACGTCGCTTTTTTTTTTTACGATCTACTaa                                                                                                                      >  2:113564/1‑140 (MQ=255)                aTTTTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAatat                                                                                                                  >  1:23962/1‑140 (MQ=255)                 ttttAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATAtt                                                                                                                 <  1:145460/140‑1 (MQ=255)                    taatCACGCATTAGAAACACTTTATTTTTTAATAGTTTTACGTTATGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCaa                                                                                                              <  1:7011/137‑1 (MQ=255)                         aCGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCt                                                                                                         >  2:88330/1‑140 (MQ=255)                                            gTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTTTTAAAatgt                                                                                      >  1:217587/1‑140 (MQ=255)                                              tttCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTAAAATTCTTTATTACTTGTTAAAatgtat                                                                                    >  1:84300/1‑140 (MQ=255)                                                      gTTTTACGTTCTGTCTTTTTTTTTTTTTTTTGATATTAAGTACATTCTATATATTCATTAAATAATTTAGGTTTCTTTGTTTTTTTACTTTCTACTATATTTTCATATTTTTTTTTTTTTTTTATTATTTATGTatatta                                                                            >  2:36216/1‑138 (MQ=255)                                                                cTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGAtgt                                                                  <  1:81569/140‑1 (MQ=255)                                                                       tttACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCa                                                           <  2:130285/140‑1 (MQ=255)                                                                                          taaGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACg                                        >  1:139287/1‑140 (MQ=255)                                                                                                cATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACAt                                  >  1:34393/1‑140 (MQ=255)                                                                                                      atatatCCATTAAATAACTTACGTCGCTTTGTTTTTTTACGTTTTACTATATATTCAATTTTTTTTTTACTTGTTTAAATGTATGTAGATAAAATTGGATGTTGTTTCATTAGTTTTTTATTATAACGGTCCATttcttt                            >  2:64292/1‑139 (MQ=255)                                                                                                      atatatCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATttcttc                            >  1:61628/1‑140 (MQ=255)                                                                                                      atatatCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATttcttc                            >  2:151149/1‑140 (MQ=255)                                                                                                       tatatCCATTAAATAACTTACGTCGCTTTGTTGTTTTACGATCCACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCa                           <  1:128539/140‑1 (MQ=255)                                                                                                                        ttACGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCAcc          >  1:69022/1‑140 (MQ=255)                                                                                                                          aCGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCCCGATCACCaa        >  1:173736/1‑140 (MQ=255)                                                                                                                          aCGGCGCTATGTTGTTTTACGGGCTACTAAATAGTCAGATTCTGTATTATTTGTTAAAATGTATGTAGATAAAACTGGATGTTGTTTCGTTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCaa        <  2:232747/140‑1 (MQ=255)                                                                                                                           cGTCGCTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAAt       <  2:126168/140‑1 (MQ=255)                                                                                                                                cTTTGTTGTTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGtt  >  1:178800/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                    ACTTAATTATTACTAATTTTAGTCACGCATTAGAAACACTTTAGTTTTCAATAGTTTTACGTTCTGTCTTTTTACCCCAGTATTGATAATAAGTACATTCTATATATCCATTAAATAACTTACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTT  >  USA300TCH1516_ALE/1514614‑1514880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑