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
A1 F70 I1 R1	12	27.5	645536	94.4%	609385	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,607	T→C	D22G (GAT→GGT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,607	0	T	C	100.0%	76.8 / NA	24	D22G (GAT→GGT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/10); total (14/10)

TAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTT  >  USA300TCH1516_ALE/1744469‑1744739

tAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATAccc                                                                                                                                    >  1:299449/1‑141 (MQ=255)

 aaGCTCCAGGCCAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCt                                                                                                                                   <  1:61514/141‑1 (MQ=255)

                   ggagaaaGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGtt                                                                                                                 <  1:111791/137‑1 (MQ=255)

                        aaGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGc                                                                                                            >  1:29539/1‑141 (MQ=255)

                                gtgttCATGTCCTACAATGATGTATTCATCTCTGTATTTTGCGTATTCTACAATTTTATCTGTGGCATAGACATATGCTTCACCATTATCCATAGTTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTg                                                                                                    <  2:233208/138‑1 (MQ=255)

                                 gcTTCAGGTCCTAGAATTTTATCAAGATCTCTGTATTTCGAGTGAATGACGATTGTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAAACTTGa                                                                                                   >  1:125203/1‑141 (MQ=255)

                                    tCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACt                                                                                                <  1:172814/141‑1 (MQ=255)

                                            tACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATAc                                                                                        >  1:251381/1‑141 (MQ=255)

                                                    tatCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTTCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCt                                                                                <  2:43657/141‑1 (MQ=255)

                                                      tCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCttt                                                                              >  1:315840/1‑141 (MQ=255)

                                                          cATCTCTGTCTTTTGCGTATTCTACAATTTTATATGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAAt                                                                          >  1:63619/1‑141 (MQ=255)

                                                                                     ttttATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTc                                               <  1:167137/141‑1 (MQ=255)

                                                                                         aTCTGTTGCATAGCCATATGCTTTACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTTGGCTAATCTTGAACTTCTGTTACGTATTCCTTTAAATCTATTAATATTTCCTCTTACATTGTTCActc                                           >  2:166418/1‑139 (MQ=255)

                                                                                         aTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGa                                           >  1:275563/1‑141 (MQ=255)

                                                                                            tGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACaa                                        >  1:147087/1‑141 (MQ=255)

                                                                                                   tAGCCATATGTTTCACTATTATTCATAATTGTAGTAGTACCCTTGAAACTATCACCTGATTTCGGCCAATTTTGAACTTATGATACGTTTTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCTCGACAATTGTGAc                                 <  2:6983/141‑1 (MQ=255)

                                                                                                               tCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAAttt                     >  1:220690/1‑141 (MQ=255)

                                                                                                                    aTTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTAt                >  1:92977/1‑141 (MQ=255)

                                                                                                                       aTCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTc             >  1:194150/1‑141 (MQ=255)

                                                                                                                         ccATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCtt           >  2:142950/1‑140 (MQ=255)

                                                                                                                         ccATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTg           <  1:197368/141‑1 (MQ=255)

                                                                                                                              aTTGTAGTAATACCCTTGAGTCTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGaaaaa      <  1:120751/141‑1 (MQ=255)

                                                                                                                              aTTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGaaaaa      <  1:35501/141‑1 (MQ=255)

                                                                                                                                tGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATACAATTTTTTATTTCTGAGACATc    >  2:179730/1‑141 (MQ=255)

                                                                                                                                  tagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCtt  >  1:183218/1‑141 (MQ=255)

TAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTT  >  USA300TCH1516_ALE/1744469‑1744739

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A