BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620540.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 14,319,331 number of mapped reads = 6,414,634 (44.8%) number of supplementary alignments = 123 (0%) number of secondary alignments = 0 number of mapped bases = 282,951,408 bp number of sequenced bases = 282,882,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,158,315 duplication rate = 8.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3045 >>>>>>> ACTG content number of A's = 74,223,698 bp (26.24%) number of C's = 51,654,393 bp (18.26%) number of T's = 87,904,079 bp (31.07%) number of G's = 69,096,045 bp (24.43%) number of N's = 4,032 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,971,890 number of insertions = 20,364 mapped reads with insertion percentage = 0.32% number of deletions = 47,244 mapped reads with deletion percentage = 0.73% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0914X std coverageData = 1.043X There is a 5.58% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 23329993 0.0936005411196147 1.4176983886371113 chr2 243199373 23930280 0.09839778657653037 1.0361963674147432 chr3 198022430 18648948 0.09417593754404488 0.673138687128531 chr4 191154276 18568969 0.09714126928554818 0.8687749515910057 chr5 180915260 17349486 0.09589841122302231 0.6507260373875159 chr6 171115067 15658158 0.09150660005877799 0.7720633978411423 chr7 159138663 15431758 0.09697051432435372 1.1263297431255828 chr8 146364022 14564180 0.09950655769762873 0.9262083643778813 chr9 141213431 11692832 0.08280254871790489 0.7611466277292025 chr10 135534747 15233051 0.11239221924396996 2.4306172554493126 chr11 135006516 13205432 0.09781329369317256 1.0497635049821565 chr12 133851895 12683692 0.09475915152340578 0.674927724028384 chr13 115169878 8673505 0.07531053388803624 0.6003204451855739 chr14 107349540 8560238 0.0797417296804439 0.6281196333612231 chr15 102531392 8332411 0.08126692554803118 0.6072110937772871 chr16 90354753 8740579 0.09673623921034902 0.831086568481716 chr17 81195210 8086286 0.09959067782446772 0.7677312170598495 chr18 78077248 7736933 0.09909331076833036 1.8623191181815815 chr19 59128983 5902988 0.09983239522316831 1.0330265637990934 chr20 63025520 6455078 0.1024200672997224 0.858454247313112 chr21 48129895 3802707 0.07900925194206221 0.7207683614329771 chr22 51304566 3528789 0.06878118801355809 0.5729918650543429 chrMT 16571 84343 5.08979542574377 6.442497494096458 chrX 155270560 9412521 0.060620126571321695 0.7197001727051829 chrY 59373566 3338251 0.05622453264808113 0.7933717235480237