BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971309.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,499,942 number of mapped reads = 5,474,529 (84.22%) number of secondary alignments = 0 number of mapped bases = 215,665,309 bp number of sequenced bases = 215,642,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,348 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.7251 >>>>>>> ACTG content number of A's = 61,933,961 bp (28.72%) number of C's = 44,706,855 bp (20.73%) number of T's = 63,295,946 bp (29.35%) number of G's = 45,693,911 bp (21.19%) number of N's = 12,245 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 708,327 number of insertions = 8,277 mapped reads with insertion percentage = 0.15% number of deletions = 18,011 mapped reads with deletion percentage = 0.33% homopolymer indels = 38.86% >>>>>>> Coverage mean coverageData = 0.0697X std coverageData = 0.6185X There is a 5.95% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 17068736 0.06848021453876338 1.1972346307968398 chr2 243199373 17526558 0.07206662494150427 0.5409659474457756 chr3 198022430 14537807 0.07341495102347749 0.3092043705436045 chr4 191154276 14631024 0.07654039609346745 0.3765762316893823 chr5 180915260 13344637 0.07376180981084736 0.315485834854041 chr6 171115067 12602123 0.07364706814508626 0.36559470720009485 chr7 159138663 12090670 0.07597569171484116 0.8440500316289217 chr8 146364022 11129408 0.07603923319352347 1.0088023330929794 chr9 141213431 8952504 0.06339697248769488 0.5490640768854463 chr10 135534747 10367222 0.07649124840289111 0.7117074332877479 chr11 135006516 9779963 0.07244067390051011 0.4530044991892386 chr12 133851895 9850747 0.07359437832389298 0.32483688391404647 chr13 115169878 6899482 0.059907001030252024 0.2706824836875068 chr14 107349540 6556592 0.061077038616094675 0.37129077278254763 chr15 102531392 5991165 0.05843249450860864 0.27271225391576237 chr16 90354753 6032435 0.0667638923211931 0.3921377930291966 chr17 81195210 5492445 0.06764493866079045 0.34001614463162 chr18 78077248 5690864 0.0728876099731384 0.9756928142306823 chr19 59128983 4315357 0.07298209407728186 1.1607998215027218 chr20 63025520 4224781 0.06703286224373872 0.314440025144864 chr21 48129895 2745819 0.05705017640283653 0.3556021435642513 chr22 51304566 2247566 0.043808303533841415 0.24093560248533633 chrMT 16571 9809 0.5919377225273067 0.9396965267959493 chrX 155270560 12662577 0.08155169273557074 0.403709878355288 chrY 59373566 915018 0.015411201678538223 0.2712829748468252