BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818746.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,097,754 number of mapped reads = 3,022,810 (97.58%) number of supplementary alignments = 19,827 (0.64%) number of secondary alignments = 0 number of mapped bases = 205,826,261 bp number of sequenced bases = 205,739,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,544,491 duplication rate = 43.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5303 >>>>>>> ACTG content number of A's = 57,558,107 bp (27.98%) number of C's = 43,082,718 bp (20.94%) number of T's = 59,892,625 bp (29.11%) number of G's = 45,193,589 bp (21.97%) number of N's = 12,743 bp (0.01%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,049,916 number of insertions = 24,989 mapped reads with insertion percentage = 0.81% number of deletions = 51,516 mapped reads with deletion percentage = 1.69% homopolymer indels = 39.35% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 0.8099X There is a 2.68% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 16931956 0.06793144960710047 1.3020246240158413 chr2 243199373 17969677 0.0738886650007934 1.3135486508094258 chr3 198022430 14010293 0.07075104067756365 0.5462953625490082 chr4 191154276 13396614 0.07008273254635433 0.6266559166302489 chr5 180915260 12664370 0.0700016681843201 0.5613872135202572 chr6 171115067 12098597 0.07070445175935325 0.6096698666760272 chr7 159138663 11120598 0.06987992603657855 0.6652672841813597 chr8 146364022 10752472 0.07346390084852956 0.6635882125190903 chr9 141213431 8833763 0.0625561105444708 0.663101380085613 chr10 135534747 9885121 0.07293421959167416 0.8383605943004175 chr11 135006516 9569517 0.07088188987855965 0.6262562876413609 chr12 133851895 9471821 0.07076344343126409 0.580057959387765 chr13 115169878 6655298 0.05778679386983461 0.5013935684174642 chr14 107349540 6372159 0.05935897815677645 0.5848453667093091 chr15 102531392 5973983 0.058264916563309704 0.5101904613289714 chr16 90354753 6254819 0.06922512421676368 0.9070346118461942 chr17 81195210 5611157 0.06910699535108043 0.5782762280779219 chr18 78077248 5547625 0.0710530294305455 0.8947940411982229 chr19 59128983 4211554 0.07122655906326006 1.0172720035971268 chr20 63025520 4562049 0.07238415486298248 0.5988288803359474 chr21 48129895 2815687 0.05850183134619346 0.5592582099393656 chr22 51304566 2471984 0.04818253408478302 0.4908685354021957 chrMT 16571 352165 21.251885824633394 16.59193788033724 chrX 155270560 6450727 0.04154507461040908 0.49441573672397326 chrY 59373566 1842255 0.031028202011649426 1.4548594192915818