BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081155.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,566,920 number of mapped reads = 2,271,595 (88.49%) number of supplementary alignments = 17,732 (0.69%) number of secondary alignments = 0 number of mapped bases = 150,836,382 bp number of sequenced bases = 150,780,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,118 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6434 >>>>>>> ACTG content number of A's = 41,649,769 bp (27.62%) number of C's = 27,791,348 bp (18.43%) number of T's = 47,256,194 bp (31.34%) number of G's = 34,039,089 bp (22.58%) number of N's = 44,500 bp (0.03%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,243,977 number of insertions = 11,538 mapped reads with insertion percentage = 0.5% number of deletions = 33,957 mapped reads with deletion percentage = 1.48% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.3814X There is a 4.19% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 12256957 0.04917523154335491 0.6478184565483588 chr2 243199373 12822777 0.052725370307595325 0.5044607681461445 chr3 198022430 10048743 0.05074547868137968 0.25373567755907517 chr4 191154276 10490376 0.05487910717728334 0.2752634075415926 chr5 180915260 9274363 0.051263575001909735 0.2560342765604681 chr6 171115067 8978004 0.05246764155490761 0.32820550930516523 chr7 159138663 8303004 0.05217464972669778 0.42981446946347057 chr8 146364022 8028968 0.05485615857153748 0.47720571820648955 chr9 141213431 5979526 0.04234389007940753 0.3506586959423788 chr10 135534747 6578227 0.0485353545537662 0.3484822130004633 chr11 135006516 6758323 0.05005923565941069 0.35315005066929445 chr12 133851895 6661981 0.049771286390827715 0.2547489437303285 chr13 115169878 5155024 0.044760175920304436 0.23895709097337353 chr14 107349540 4326578 0.04030364731884273 0.2450338995735059 chr15 102531392 4355823 0.042482823211841304 0.23758654935629953 chr16 90354753 4038265 0.044693442966968214 0.2619622394221279 chr17 81195210 3618972 0.04457124995427686 0.2792354582471005 chr18 78077248 4135104 0.0529617027485395 0.6522995437281013 chr19 59128983 2753640 0.04657005516228818 0.4644108510052983 chr20 63025520 2788795 0.044248663081240744 0.2480768348162778 chr21 48129895 1948004 0.040473888422154256 0.24050940586459657 chr22 51304566 1568314 0.030568702208688403 0.19502976701241637 chrMT 16571 154512 9.324241144167521 5.842531404385605 chrX 155270560 9437095 0.06077839224641168 0.3125027050235868 chrY 59373566 375007 0.006316059911240636 0.12597450322404632