BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231806.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 = 11,482,564 number of mapped reads = 9,993,385 (87.03%) number of supplementary alignments = 79,437 (0.69%) number of secondary alignments = 0 number of mapped bases = 652,143,480 bp number of sequenced bases = 651,903,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 865,674 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5657 >>>>>>> ACTG content number of A's = 188,841,053 bp (28.97%) number of C's = 128,214,301 bp (19.67%) number of T's = 188,735,344 bp (28.95%) number of G's = 146,063,405 bp (22.41%) number of N's = 49,210 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 4,031,278 number of insertions = 47,994 mapped reads with insertion percentage = 0.48% number of deletions = 144,139 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.2107X std coverageData = 17.5659X There is a 13.93% of reference with a coverageData >= 1X There is a 4.12% of reference with a coverageData >= 2X There is a 1.33% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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% 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 65825258 0.26409265395571474 4.65495527218387 chr2 243199373 54008622 0.22207549852523675 62.284991928150035 chr3 198022430 52366553 0.26444758303390176 0.7148918987158005 chr4 191154276 21331587 0.11159356435217803 0.714315340705694 chr5 180915260 29119611 0.16095718514845017 0.5967320868750299 chr6 171115067 37458740 0.21890965335039725 0.9141508774914406 chr7 159138663 50796524 0.3191966241415513 3.468813453676671 chr8 146364022 46647910 0.31871158883567713 2.5325647611267756 chr9 141213431 28301246 0.20041469001627757 1.6024339902703288 chr10 135534747 31375379 0.23149324947646083 1.5424142322420815 chr11 135006516 24773032 0.18349508404468418 1.6688587097042002 chr12 133851895 21001974 0.15690456978588163 0.6443777690754176 chr13 115169878 19907618 0.17285438124715213 0.5706236510948199 chr14 107349540 27048984 0.2519711216275356 1.0322690561761214 chr15 102531392 11495879 0.11212057864190511 0.46684667515110495 chr16 90354753 15785043 0.1747007487254157 0.9172460223500573 chr17 81195210 15762354 0.1941291118035165 0.8870518731434915 chr18 78077248 19619292 0.25128052669069484 3.5420690726379718 chr19 59128983 14629835 0.24742240197163548 2.595074351801572 chr20 63025520 13857952 0.2198784238511638 0.7475854147684934 chr21 48129895 9845003 0.20455068518225522 0.7772474561631527 chr22 51304566 5545283 0.1080855649378264 0.43077570067589344 chrMT 16571 224865 13.569790598032707 9.8226733757515 chrX 155270560 33798251 0.21767327302741743 0.9926266941761305 chrY 59373566 1616685 0.02722903657159484 0.5751143501485462