BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975241.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,359,882 number of mapped reads = 2,333,452 (98.88%) number of supplementary alignments = 9,592 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,166,571 number of mapped paired reads (second in pair) = 1,166,881 number of mapped paired reads (both in pair) = 2,324,706 number of mapped paired reads (singletons) = 8,746 number of mapped bases = 212,915,218 bp number of sequenced bases = 212,792,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,604 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 39,975.6574 std insert size = 1,878,842.5112 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.8676 >>>>>>> ACTG content number of A's = 62,118,679 bp (29.19%) number of C's = 40,185,445 bp (18.88%) number of T's = 65,424,598 bp (30.75%) number of G's = 45,060,696 bp (21.18%) number of N's = 2,848 bp (0%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,692,430 number of insertions = 36,398 mapped reads with insertion percentage = 1.52% number of deletions = 69,601 mapped reads with deletion percentage = 2.92% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.0688X std coverageData = 0.7642X There is a 5.1% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14514114 0.05823100436728701 1.0230437779050687 chr2 243199373 22312588 0.09174607534863999 1.1575115206546638 chr3 198022430 13522435 0.06828739047389733 0.32727768384664063 chr4 191154276 11227772 0.05873670333171098 0.703083411177763 chr5 180915260 13227475 0.07311420274884496 0.3346298224894416 chr6 171115067 10670470 0.062358447955959365 0.4366657272612161 chr7 159138663 8867394 0.05572117945970176 0.6670723420144249 chr8 146364022 14143527 0.09663253856196982 0.4861113738366192 chr9 141213431 10554343 0.0747403623384804 1.2968791317377317 chr10 135534747 10837824 0.07996343550189385 1.4085132288593536 chr11 135006516 12429983 0.09206950426007586 0.5828403054692403 chr12 133851895 11047860 0.08253794240268321 0.3502147344238003 chr13 115169878 7110496 0.061739198855450726 0.2989053132732386 chr14 107349540 7370435 0.06865828209417572 0.35688862048759196 chr15 102531392 3103112 0.03026499435411937 0.20858006010832605 chr16 90354753 5625865 0.062264184375557974 0.9644839256760823 chr17 81195210 4515769 0.05561619952704107 0.9666027870703514 chr18 78077248 6000155 0.07684895604927058 1.0960152967539918 chr19 59128983 3186257 0.053886551710182466 0.5035447321593427 chr20 63025520 10255359 0.1627175626635052 0.5334516165856077 chr21 48129895 2081520 0.043247964700525526 0.3147330888043336 chr22 51304566 1688366 0.032908688867965476 0.2305225334781878 chrMT 16571 86972 5.248446080502082 4.267396456309413 chrX 155270560 6299305 0.040569860764332916 0.32095454886511837 chrY 59373566 2235822 0.03765685894628596 0.7962527124145646