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 F184 I0 R1	35	35.7	768239	98.7%	758251	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,241,539	T→C	57.6%	intergenic (‑182/+284)	murA2 ← / ← fba	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase 2/Fructose‑bisphosphate aldolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,241,539	0	T	C	57.6%	1.0 / 35.2	31	intergenic (‑182/+284)	murA2/fba	UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase 2/Fructose‑bisphosphate aldolase
Reads supporting (aligned to +/- strand): ref base T (8/5); new base C (9/9); total (17/14)
Fisher's exact test for biased strand distribution p-value = 7.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.71e-02

TAAATTAATTTTACTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATCACAATCAATTT  >  USA300TCH1516_ALE/2241411‑2241670

taatttaattTTATTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTc                                                                                                                          <  1:103354/140‑1 (MQ=255)

      aattTTACTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATAATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGatta                                                                                                                    >  1:233532/1‑140 (MQ=255)

            aCTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAAc                                                                                                              >  1:66800/1‑140 (MQ=255)

            aCTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAAc                                                                                                              >  1:601399/1‑140 (MQ=255)

             cTTTTTTTGTAAAATAGTTTGTTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACt                                                                                                             <  1:171934/140‑1 (MQ=255)

                 aTTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAat                                                                                                         <  1:183672/140‑1 (MQ=255)

                     gTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTg                                                                                                     <  1:504570/140‑1 (MQ=255)

                        taaTAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCGTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACg                                                                                                  <  1:596112/139‑1 (MQ=255)

                            aGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTGCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACgttgt                                                                                              <  1:163534/140‑1 (MQ=255)

                                    ttAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTGTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAGCTAAATATTGACGTTGTTTTGACaa                                                                                      >  1:470000/1‑140 (MQ=255)

                                       aTCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTAACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAatta                                                                                   >  1:69080/1‑140 (MQ=255)

                                                   ttGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAAt                                                                       >  1:164805/1‑140 (MQ=255)

                                                   ttGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAAt                                                                       >  1:644440/1‑140 (MQ=255)

                                                      tCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTATTATATGCTGTTCTTCCCCAATTGACCACGGTCTAAATTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCt                                                                    <  1:407784/140‑1 (MQ=255)

                                                      tCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCt                                                                    <  1:85352/140‑1 (MQ=255)

                                                                   gattgattAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGt                                                       <  1:39302/140‑1 (MQ=255)

                                                                      tgattAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTTACGTaaa                                                    >  1:728925/1‑140 (MQ=255)

                                                                             taaCAAATCATTCATCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACcttttt                                             <  1:25852/140‑1 (MQ=255)

                                                                                    tCATTCACCGTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTGGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATaact                                      >  1:561507/1‑138 (MQ=255)

                                                                                     cATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAATTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAAtt                                     >  1:99515/1‑140 (MQ=255)

                                                                                       ttCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGCTTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGc                                   >  1:118303/1‑140 (MQ=255)

                                                                                            cTTTACTAATATATGCTGTTCTTCCCAACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTGAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCAtt                              <  1:636315/140‑1 (MQ=255)

                                                                                               tACTAATATATGCTGTTCTTCCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTc                           <  1:290191/140‑1 (MQ=255)

                                                                                                           cTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTACTTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATtata               >  1:289918/1‑140 (MQ=255)

                                                                                                           cTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATATTCCTTATAATtata               >  1:158402/1‑140 (MQ=255)

                                                                                                             gTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGTCTATTTTCCTTATAATTATATc             >  1:216524/1‑140 (MQ=255)

                                                                                                                cctcCCCACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATcaca          <  1:449301/138‑1 (MQ=255)

                                                                                                                 ttcCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATCAcaa         <  1:577866/140‑1 (MQ=255)

                                                                                                                   ccccACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCAAGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATCAcaatc       >  1:399942/1‑140 (MQ=255)

                                                                                                                     ccACTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGCCGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATCAcaatcaa     >  1:222571/1‑140 (MQ=255)

                                                                                                                        cTTGACCACGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATGTCACAATCAAttt  >  1:546432/1‑140 (MQ=255)

TAAATTAATTTTACTTTATTTGTAAAATAGTTTATTTTAATCGTTAAAATCTTGTCTTTCTATTTTCGATTGATTAATAACAAATCATTCACCTTTACTAATATATGCTGTTCTTCCCCACTTGACCATGGTCTAAAGTCTGATTATTCAACTAAATATTGACGTTGTTTTGACAATTATTTAGTTTTAATTCTACGGTTTTCACGTAAACTTTTTTCATAAATTGCTCATTTTCCTTATAATTATATCACAATCAATTT  >  USA300TCH1516_ALE/2241411‑2241670

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