BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234147.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 = 1,333,316 number of mapped reads = 251,524 (18.86%) number of supplementary alignments = 2,474 (0.19%) number of secondary alignments = 0 number of mapped bases = 15,614,687 bp number of sequenced bases = 15,606,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,152 duplication rate = 9.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1624 >>>>>>> ACTG content number of A's = 4,282,605 bp (27.44%) number of C's = 2,749,440 bp (17.62%) number of T's = 5,094,423 bp (32.64%) number of G's = 3,473,595 bp (22.26%) number of N's = 6,353 bp (0.04%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 153,972 number of insertions = 2,086 mapped reads with insertion percentage = 0.81% number of deletions = 4,735 mapped reads with deletion percentage = 1.85% homopolymer indels = 39.61% >>>>>>> Coverage mean coverageData = 0.005X std coverageData = 0.1525X There is a 0.3% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 1221070 0.0048989647251470635 0.12959204397606128 chr2 243199373 1339960 0.005509718152110532 0.28519273524986444 chr3 198022430 1134406 0.0057286742718994 0.12911258039361542 chr4 191154276 1071195 0.005603824420856795 0.13392071097065036 chr5 180915260 986784 0.005454398926878805 0.13005813352107584 chr6 171115067 916267 0.005354683348836839 0.12564649568082356 chr7 159138663 882032 0.005542537453641922 0.1363841304994705 chr8 146364022 882944 0.00603252075158197 0.17283354363457568 chr9 141213431 600528 0.004252626649939552 0.11027201866727293 chr10 135534747 825464 0.006090423439533185 0.14192274606489924 chr11 135006516 647251 0.004794220450811426 0.11807279704637419 chr12 133851895 722572 0.005398294884058234 0.12794230862764572 chr13 115169878 485997 0.004219827340617657 0.12464708009103295 chr14 107349540 526191 0.004901660500827484 0.13612951443170235 chr15 102531392 447334 0.0043628979503174984 0.18554813040084392 chr16 90354753 409731 0.0045346922701454346 0.12101030359858242 chr17 81195210 345900 0.004260103520885038 0.11086989607942078 chr18 78077248 434652 0.005566948261291177 0.25226186920186894 chr19 59128983 260578 0.004406942023677289 0.11255753861508767 chr20 63025520 313752 0.004978173920659441 0.11997247234011121 chr21 48129895 204243 0.004243578757028246 0.10975707981173304 chr22 51304566 144174 0.0028101592361194517 0.08863326731546953 chrMT 16571 7228 0.43618369440588983 1.0119455565772542 chrX 155270560 732243 0.004715916526610067 0.12126086227591296 chrY 59373566 72191 0.0012158777864209806 0.052820621606633714