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 F8 I0 R1	311	50.1	4085234	95.9%	3917739	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,544,281	T→C	24.2%	intergenic (‑98/‑1358)	yjhA ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,544,281	0	T	C	24.2%	55.6 / 16.8	33	intergenic (‑98/‑1358)	yjhA/fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand): ref base T (12/13); new base C (6/2); total (18/15)
Fisher's exact test for biased strand distribution p-value = 2.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCT  >  W3110S.gb/4544212‑4544343

aGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTc                                                               <  1:637555/71‑1 (MQ=255)

      aCAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTgg                                                          >  1:3995450/1‑70 (MQ=255)

       cAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGc                                                         >  1:1797735/1‑70 (MQ=255)

       cAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGc                                                         >  1:3606808/1‑70 (MQ=255)

       cAAAGCCCGCATAAACAATTAGCATTTATGGTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGc                                                         >  1:939162/1‑70 (MQ=255)

                  tAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTg                                             >  1:1346858/1‑71 (MQ=255)

                    aaCAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCgg                                                   >  1:1143013/1‑63 (MQ=255)

                    aaCAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCgg                                                   >  1:1385523/1‑63 (MQ=255)

                      cAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTAtt                                         >  1:180034/1‑71 (MQ=255)

                      cAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTAtt                                         >  1:4065841/1‑71 (MQ=255)

                      cAATCAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTg                                             >  1:996138/1‑67 (MQ=255)

                         ttAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTta                                      <  1:755792/71‑1 (MQ=255)

                          tAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCTAcc                                                     <  1:2877414/55‑1 (MQ=255)

                          tAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTATTTta                                      >  1:3052995/1‑70 (MQ=255)

                          tAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTATTTta                                      >  1:120488/1‑70 (MQ=255)

                               tttATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCgg                                                   <  1:2585388/52‑1 (MQ=255)

                                 tATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCtttc                                                           >  1:3586167/1‑41 (MQ=255)

                                     ttgtGTAATATTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGt                           <  1:3278045/70‑1 (MQ=255)

                                       gtgtAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtat                         <  1:3050041/70‑1 (MQ=255)

                                       gtgtAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtat                         <  1:3955319/70‑1 (MQ=255)

                                        tgtAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtata                        <  1:2127246/70‑1 (MQ=255)

                                          tAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAgg                     >  1:1231662/1‑71 (MQ=255)

                                            atatTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGtc                   >  1:3905469/1‑71 (MQ=255)

                                            atatTTTTTTGCCAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGt                    >  1:2097204/1‑70 (MQ=255)

                                             tatTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGt                           <  1:3378692/62‑1 (MQ=255)

                                               tttttttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtata                        <  1:3811957/63‑1 (MQ=255)

                                               tttttttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtata                        <  1:3816759/63‑1 (MQ=255)

                                               tttttttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGtctc                 <  1:707125/70‑1 (MQ=255)

                                               tttttttGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATATTTTCGtat                         >  1:302541/1‑62 (MQ=255)

                                                       ccAGGCTTATAGTGCCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGaaaa        <  1:502354/71‑1 (MQ=255)

                                                           gCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATAtt                                  <  1:2950838/41‑1 (MQ=255)

                                                           gCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtat                         <  1:1130300/50‑1 (MQ=255)

                                                             ttATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATctct  >  1:2630758/1‑71 (MQ=255)

                                                                  gtgtCTTTGGCAACCGGTAGCTGTATTTTATAttttttt                             >  1:3463304/1‑39 (MQ=255)

                                                                     tCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtata                        <  1:1250095/41‑1 (MQ=255)

                                                                     tCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGtat                         <  1:3008343/40‑1 (MQ=255)

AGCAATACAAAGCCCGCATAAACAATTAGCATTTATGTTGTGTAATATTTTTTTGCCAGGCTTATAGTGTCTTTGGCAACCGGTAGCTGTATTTTATATTTTTTTGTATAAGGTCTCCTGTGAAAAATCTCT  >  W3110S.gb/4544212‑4544343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A