Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A7 F67 I1 R1	28	23.6	502806	98.6%	495766	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,184,430	G→T	T172K (ACA→AAA)	rpsA_2 ←	30S ribosomal protein S1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,184,430	0	G	T	100.0%	62.4 / NA	19	T172K (ACA→AAA)	rpsA_2	30S ribosomal protein S1
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (8/11); total (8/11)

AAACTCTATGATTAGCAATGCGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTGTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGC  >  USA300TCH1516_ALE/2184293‑2184566

aacccctATGATTAGCAATGCGTTTAATTGGATCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCGTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTc                                                                                                                                       <  1:29768/136‑1 (MQ=255)

                    cGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGaa                                                                                                                   <  1:393927/141‑1 (MQ=255)

                                   cTATATGCATAGTACATTTCAAAAATACCTTTTTCATCCTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAACTTTGTTCCGCaata                                                                                                    <  1:326207/141‑1 (MQ=255)

                                           aTAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTtg                                                                                            <  1:485306/141‑1 (MQ=255)

                                           aTAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTtg                                                                                            <  1:139985/141‑1 (MQ=255)

                                                    ttCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCttt                                                                                   >  1:418445/1‑141 (MQ=255)

                                                             aCCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTTTGCACCTTTGATAGCATc                                                                          <  1:497872/141‑1 (MQ=255)

                                                              ccTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCt                                                                         >  1:62525/1‑141 (MQ=255)

                                                                       tCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGGTGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCATTAATGTCTTGTGCACCTTTGATAGCCTCTTCAACCGAt                                                                >  1:184749/1‑141 (MQ=255)

                                                                        cTTCAGCATTTTTCTATTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGAtt                                                               >  1:371232/1‑141 (MQ=255)

                                                                          tCAGCATTTTTCTTTCTATATGCAGCTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGc                                                             <  1:134902/141‑1 (MQ=255)

                                                                             gCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCAct                                                          <  1:265266/141‑1 (MQ=255)

                                                                                tttttCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCAattct                                                       >  1:106344/1‑141 (MQ=255)

                                                                                               gTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCTACCGATTGCACTTCTTCATTtattagtggt                                        >  1:126076/1‑134 (MQ=255)

                                                                                                  gTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATtgttgt                                     <  1:218092/141‑1 (MQ=255)

                                                                                                        acacCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATGATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGTACTTCCTCATTTATAAATTGTTGTGCtttt                               >  1:62515/1‑141 (MQ=255)

                                                                                                        acacCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGAAGTAGCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCtttt                               >  1:390627/1‑141 (MQ=255)

                                                                                                                          tCTTTTAAATTTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCa             <  1:212118/141‑1 (MQ=255)

                                                                                                                          tCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCa             <  1:44460/141‑1 (MQ=255)

                                                                                                                                     ttttttTCTATATTTAGGTTTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATTAGTTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGc  >  1:104139/1‑141 (MQ=255)

AAACTCTATGATTAGCAATGCGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTGTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGC  >  USA300TCH1516_ALE/2184293‑2184566

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: `‑`

GATK/CNVnator alignment

N/A