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
A13 F55 I1 R1	12	36.0	825780	91.1%	752285	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,484	A→T	L431* (TTA→TAA)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,484	0	A	T	100.0%	97.5 / NA	29	L431* (TTA→TAA)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (17/12); total (17/12)

TTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGCACTGC  >  USA300TCH1516_ALE/2372361‑2372626

ttATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTActt                                                                                                                        <  1:151064/148‑1 (MQ=255)

              aTTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTa                                                                                                          <  2:235806/148‑1 (MQ=255)

                tttATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTaga                                                                                                        <  1:158842/148‑1 (MQ=255)

                 ttATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTagag                                                                                                       >  1:235179/1‑148 (MQ=255)

                 ttATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTagag                                                                                                       >  2:144668/1‑148 (MQ=255)

                 ttATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCACTCGTATTTTCTGTCTGGATTTAACCATTAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTagag                                                                                                       >  2:47728/1‑148 (MQ=255)

                    tCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATa                                                                                                    >  1:162712/1‑148 (MQ=255)

                                            cTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaata                                                                            >  1:341320/1‑148 (MQ=255)

                                            cTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaata                                                                            >  1:73989/1‑148 (MQ=255)

                                               ccAATCATTGGCAGTCGTTTTTTGTGTCTGTATTTTACTTTGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaataaat                                                                         >  2:209183/1‑148 (MQ=255)

                                               ccAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACAATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAaaataaat                                                                         >  2:307662/1‑148 (MQ=255)

                                                                     tgtgTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCaa                                                   <  1:338711/148‑1 (MQ=255)

                                                                             gATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAatat                                           <  2:398841/148‑1 (MQ=255)

                                                                             gATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAatat                                           <  2:195787/148‑1 (MQ=255)

                                                                                 tAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATa                                       <  2:64576/148‑1 (MQ=255)

                                                                                 tAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATa                                       >  1:312929/1‑148 (MQ=255)

                                                                                 tAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATa                                       >  1:217617/1‑148 (MQ=255)

                                                                                      aTGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGATATAATTATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGc                                  >  2:205429/1‑148 (MQ=255)

                                                                                         aaCAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGcatc                               <  2:146709/148‑1 (MQ=255)

                                                                                            aaaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATa                            >  2:284764/1‑148 (MQ=255)

                                                                                            aaaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATa                            >  1:153358/1‑148 (MQ=255)

                                                                                            aaaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATa                            >  2:227426/1‑148 (MQ=255)

                                                                                            aaaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATa                            >  1:388636/1‑148 (MQ=255)

                                                                                             aaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTTGTTATTATCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATaa                           >  2:293411/1‑148 (MQ=255)

                                                                                             aaTATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATaa                           >  2:75278/1‑148 (MQ=255)

                                                                                                 tGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGAATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGAt                       <  1:371449/148‑1 (MQ=255)

                                                                                                    aGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGt                    <  2:6347/148‑1 (MQ=255)

                                                                                                    aGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGt                    <  1:342284/148‑1 (MQ=255)

                                                                                                                      ccATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGCACTGc  <  2:221279/148‑1 (MQ=255)

TTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGCACTGC  >  USA300TCH1516_ALE/2372361‑2372626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A