BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927041.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,413,286 number of mapped reads = 30,595,649 (97.4%) number of supplementary alignments = 720,274 (2.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,361,988 number of mapped paired reads (second in pair) = 15,233,661 number of mapped paired reads (both in pair) = 30,109,288 number of mapped paired reads (singletons) = 486,361 number of mapped bases = 2,776,794,819 bp number of sequenced bases = 2,774,714,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,185,264 duplication rate = 7.9% >>>>>>> Insert size mean insert size = 235,756.4897 std insert size = 4,818,758.4107 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.8186 >>>>>>> ACTG content number of A's = 783,052,952 bp (28.22%) number of C's = 546,990,421 bp (19.71%) number of T's = 802,812,283 bp (28.93%) number of G's = 641,511,475 bp (23.12%) number of N's = 347,770 bp (0.01%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 28,689,373 number of insertions = 467,624 mapped reads with insertion percentage = 1.5% number of deletions = 1,435,404 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.96% >>>>>>> Coverage mean coverageData = 0.897X std coverageData = 4.3066X There is a 34.11% of reference with a coverageData >= 1X There is a 19.36% of reference with a coverageData >= 2X There is a 11.41% of reference with a coverageData >= 3X There is a 7.2% of reference with a coverageData >= 4X There is a 4.7% of reference with a coverageData >= 5X There is a 3.17% of reference with a coverageData >= 6X There is a 2.19% of reference with a coverageData >= 7X There is a 1.54% of reference with a coverageData >= 8X There is a 1.1% of reference with a coverageData >= 9X There is a 0.8% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 220011730 0.8826928058084959 3.1309733627580654 chr2 243199373 241999471 0.9950661797142051 5.675644070961994 chr3 198022430 183722490 0.927786261384632 1.9034553281570288 chr4 191154276 153122599 0.8010419761679828 2.1975342749581963 chr5 180915260 161237862 0.8912341722859641 1.880746058976497 chr6 171115067 156192773 0.9127938044170009 1.9020626897463802 chr7 159138663 143081158 0.8990973991028189 2.2213996567287237 chr8 146364022 137496116 0.9394119819965046 2.179250433086839 chr9 141213431 126538328 0.8960785606859166 3.552876863886772 chr10 135534747 140915795 1.0397023502762728 4.454152000637403 chr11 135006516 132925934 0.9845890253178595 2.5097943953107147 chr12 133851895 126247102 0.9431850180380338 1.9546549576377208 chr13 115169878 77468849 0.6726485288106322 1.6214937478800715 chr14 107349540 81301532 0.7573533337916493 1.7961326303428202 chr15 102531392 92083656 0.8981020758988623 1.995563682199524 chr16 90354753 89066685 0.9857443249277655 3.5947077574699398 chr17 81195210 77998534 0.9606297465084455 2.4205147712805783 chr18 78077248 74040447 0.9482973452138067 3.421078447130129 chr19 59128983 51211285 0.8660944667355432 2.3706746571629234 chr20 63025520 71539393 1.1350861206698493 2.2914385183351937 chr21 48129895 33437933 0.6947435268662024 2.252784701576139 chr22 51304566 39061451 0.761364027521449 1.9430488473217145 chrMT 16571 17770162 1072.3650956490253 857.9872303542236 chrX 155270560 144197090 0.9286827457825875 2.0547531834193475 chrY 59373566 4126444 0.06949968273760077 2.1646962830657417