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
A2 F28 I3 R2	122	64.1	3058059	97.6%	2984665	63.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	1,099,149	A→G	T130A (ACA→GCA)	ydiM →	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,099,149	0	A	G	96.4%	90.0 / ‑3.0	28	coding (388/1215 nt)	ydiM	predicted transporter
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (16/11); minor base . (1/0); total (17/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

GCAAACAGTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGACAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTTTATTACCGCTAATCATT  >  minE/1099083‑1099211

gCAAACAGTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTGACCTGGGGCAGc                                                            >  1:1413847/1‑71 (MQ=255)

gCAAACAGTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGc                                                            >  1:158715/1‑71 (MQ=255)

 cAAACAGTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGcc                                                           <  1:1864218/71‑1 (MQ=255)

       gTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAatat                                                      <  1:2200469/70‑1 (MQ=255)

          ttCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCa                                                              >  1:786987/1‑59 (MQ=255)

          ttCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATAtttt                                                   >  1:1776910/1‑70 (MQ=255)

          ttCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGG‑CAGCCAATATTttaa                                                 >  1:2017238/1‑71 (MQ=255)

             tcGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAatat                                                      <  1:63053/64‑1 (MQ=255)

             tcGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAatat                                                      <  1:2580629/64‑1 (MQ=255)

                         cTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGtt                                   >  1:2740968/1‑71 (MQ=255)

                           tATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCa                                                              >  1:1328918/1‑42 (MQ=255)

                            aTCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTttaat                                                >  1:1827366/1‑55 (MQ=255)

                             tCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCa                               <  1:2089552/71‑1 (MQ=255)

                               ccAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGc                             >  1:2233324/1‑71 (MQ=255)

                                cAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAg                              >  1:303466/1‑69 (MQ=255)

                                  gTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCAtt                                       <  1:1213765/58‑1 (MQ=255)

                                  gTTTGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGa                          >  1:137580/1‑71 (MQ=255)

                                     tGATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGttt                                  >  1:1470736/1‑60 (MQ=255)

                                      gATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACaa                       <  1:412110/70‑1 (MQ=255)

                                      gATGGAAGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACaa                       <  1:1191882/70‑1 (MQ=255)

                                           aaGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTtta                 >  1:1755902/1‑71 (MQ=255)

                                            aGCTTTTCCACGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTttat                >  1:3020983/1‑71 (MQ=255)

                                                     aCGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAAttt                    >  1:2231814/1‑58 (MQ=255)

                                                     aCGCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAAtt                     >  1:355498/1‑57 (MQ=255)

                                                       gCTCACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTTTATTACCGCTAATc     <  1:91988/71‑1 (MQ=255)

                                                          cACCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAAtttt                   >  1:2811815/1‑54 (MQ=255)

                                                           aCCTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTTTATTACCGCTAATCAtt  <  1:1277922/70‑1 (MQ=255)

                                                            ccTGGGGCAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTTTATTACCGCTAATCAt   <  1:1450711/68‑1 (MQ=255)

GCAAACAGTTTTCTCGATGCAGGCACTTATCCCAGTTTGATGGAAGCTTTTCCACGCTCACCTGGGACAGCCAATATTTTAATTAAAGCATTTGTTTCCAGCGGACAATTTTTATTACCGCTAATCATT  >  minE/1099083‑1099211

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A