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 F15 I1 R1	10	32.9	697396	98.3%	685540	149.0

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%	107.7 / NA	28	D22G (GAT→GGT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/14); total (14/14)

ATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATATAAT  >  USA300TCH1516_ALE/1744468‑1744747

aTAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAAc                                                                                                                                     >  4:78332/1‑149 (MQ=255)

  aaGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTa                                                                                                                                   >  4:76179/1‑149 (MQ=255)

        cAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCt                                                                                                                             <  4:148074/149‑1 (MQ=255)

           gACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGt                                                                                                                          >  4:170076/1‑149 (MQ=255)

                          aGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGa                                                                                                           <  4:279297/149‑1 (MQ=255)

                            ccACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAAc                                                                                                         >  4:101098/1‑149 (MQ=255)

                                       aGGTCCTACAACGCTATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTCTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACTCCTGGTTTCGGCCAATCTTCAACTTCTGATACGt                                                                                              <  4:172449/149‑1 (MQ=255)

                                       aGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGt                                                                                              <  4:87179/149‑1 (MQ=255)

                                         gTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTAt                                                                                            >  4:273729/1‑149 (MQ=255)

                                             tACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCt                                                                                        <  3:141208/149‑1 (MQ=255)

                                                 aCGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTaa                                                                                    <  4:10711/149‑1 (MQ=255)

                                                       tCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCAt                                                                              <  3:253105/149‑1 (MQ=255)

                                                                ctGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTtc                                                                     <  4:73232/149‑1 (MQ=255)

                                                                          cGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAAtt                                                           >  4:96131/1‑149 (MQ=255)

                                                                                 tACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACg                                                    >  3:51322/1‑149 (MQ=255)

                                                                                      ttttATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAAt                                               <  4:194727/149‑1 (MQ=255)

                                                                                         tATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATtgt                                            >  3:240766/1‑149 (MQ=255)

                                                                                              gTTGCATNGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACtt                                       <  4:231876/149‑1 (MQ=255)

                                                                                               ttGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACttt                                      >  4:104220/1‑149 (MQ=255)

                                                                                               ttGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACttt                                      >  3:176168/1‑149 (MQ=255)

                                                                                               ttGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACttt                                      >  2:24205/1‑149 (MQ=255)

                                                                                                        cATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAAttt                             <  4:254781/149‑1 (MQ=255)

                                                                                                                        aTCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAAt             <  3:125179/149‑1 (MQ=255)

                                                                                                                            aTAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTg         <  3:78332/149‑1 (MQ=255)

                                                                                                                            aTAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAA‑TTTTTATTTCTGAAAAATCTTGa        <  4:109891/149‑1 (MQ=255)

                                                                                                                               aTTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGata      >  4:95150/1‑149 (MQ=255)

                                                                                                                                   tagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATataat  >  4:230534/1‑149 (MQ=255)

                                                                                                                                   tagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATataat  >  4:230535/1‑149 (MQ=255)

ATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATATAAT  >  USA300TCH1516_ALE/1744468‑1744747

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

GATK/CNVnator alignment

N/A