BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008791.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,256,701 number of mapped reads = 1,018,393 (81.04%) number of supplementary alignments = 7,404 (0.59%) number of secondary alignments = 0 number of mapped bases = 65,171,421 bp number of sequenced bases = 65,135,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,204 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6263 >>>>>>> ACTG content number of A's = 17,526,909 bp (26.91%) number of C's = 11,741,560 bp (18.03%) number of T's = 20,946,102 bp (32.16%) number of G's = 14,895,511 bp (22.87%) number of N's = 25,062 bp (0.04%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 563,419 number of insertions = 4,320 mapped reads with insertion percentage = 0.42% number of deletions = 21,245 mapped reads with deletion percentage = 2.06% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.2412X There is a 1.82% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 5023666 0.020155079172300236 0.45601714682290695 chr2 243199373 6543894 0.026907528252550224 0.2742406383388048 chr3 198022430 6434527 0.03249393010680659 0.20935172392491955 chr4 191154276 3712138 0.019419591743791282 0.16439190433021664 chr5 180915260 2813662 0.015552375183829159 0.14004456237919768 chr6 171115067 2906002 0.01698273595042335 0.16188960672632233 chr7 159138663 4183806 0.026290317645813074 0.2581631423057645 chr8 146364022 5285997 0.036115412297155924 0.2745946503462936 chr9 141213431 2440340 0.017281217393549486 0.20763829356704705 chr10 135534747 4562300 0.03366147870553077 0.3661532429308007 chr11 135006516 2193726 0.016249037935324544 0.18218137862126474 chr12 133851895 1667393 0.012456999581515077 0.12752983234837018 chr13 115169878 1992393 0.017299601550328985 0.14670371899253892 chr14 107349540 1855685 0.01728638054713602 0.15208574351869886 chr15 102531392 1730858 0.016881249403109633 0.1453595199046311 chr16 90354753 1433116 0.01586099183957705 0.1655874282191976 chr17 81195210 1265013 0.015579896892932477 0.1495957226830105 chr18 78077248 1353098 0.017330247090676147 0.3185135403146425 chr19 59128983 1034518 0.01749595456427857 0.31757539294210396 chr20 63025520 1534936 0.0243541981089565 0.17813324882211232 chr21 48129895 578190 0.012013115756849251 0.13194409214984162 chr22 51304566 609038 0.011871029178962355 0.12059130007130504 chrMT 16571 5163 0.3115684026311025 0.5985303918507053 chrX 155270560 3799331 0.024469100903609802 0.18697315407539045 chrY 59373566 212631 0.003581240176815386 0.12955161849058303