BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173949.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 13,559,072 number of mapped reads = 13,207,738 (97.41%) number of supplementary alignments = 1,814,580 (13.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,611,210 number of mapped paired reads (second in pair) = 6,596,528 number of mapped paired reads (both in pair) = 12,981,610 number of mapped paired reads (singletons) = 226,128 number of mapped bases = 1,496,459,652 bp number of sequenced bases = 1,495,386,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,774,947 duplication rate = 65.51% >>>>>>> Insert size mean insert size = 1,149,904.3852 std insert size = 9,831,559.657 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.4761 >>>>>>> ACTG content number of A's = 444,442,748 bp (29.72%) number of C's = 298,792,176 bp (19.98%) number of T's = 440,874,303 bp (29.48%) number of G's = 311,266,986 bp (20.82%) number of N's = 10,725 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 13,139,231 number of insertions = 170,942 mapped reads with insertion percentage = 1.24% number of deletions = 454,833 mapped reads with deletion percentage = 3.36% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 0.4834X std coverageData = 8.5319X There is a 9.69% of reference with a coverageData >= 1X There is a 7.44% of reference with a coverageData >= 2X There is a 5.71% of reference with a coverageData >= 3X There is a 4.63% of reference with a coverageData >= 4X There is a 3.55% of reference with a coverageData >= 5X There is a 2.93% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.92% of reference with a coverageData >= 8X There is a 1.48% of reference with a coverageData >= 9X There is a 1.31% of reference with a coverageData >= 10X There is a 1% of reference with a coverageData >= 11X There is a 0.91% of reference with a coverageData >= 12X There is a 0.69% of reference with a coverageData >= 13X There is a 0.64% of reference with a coverageData >= 14X There is a 0.48% of reference with a coverageData >= 15X There is a 0.44% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 124106852 0.49791993095977083 3.8565375957882453 chr2 243199373 134626418 0.5535640011703484 28.448050894506995 chr3 198022430 99890298 0.5044393102336943 2.1855591998893953 chr4 191154276 101181696 0.5293195533852457 3.765499154084468 chr5 180915260 95477241 0.5277456473268203 2.24562679224209 chr6 171115067 89891243 0.525326288187118 2.816936983473685 chr7 159138663 81303114 0.510894791167122 3.4286824210384257 chr8 146364022 76801165 0.5247270739799703 4.854674871095124 chr9 141213431 63729162 0.45129674669543296 3.3653255872058 chr10 135534747 73082697 0.5392174229682961 4.763032530149395 chr11 135006516 70486834 0.5220994962939418 2.3920289424614767 chr12 133851895 66710968 0.49839390021336644 2.311620413854301 chr13 115169878 47773875 0.4148122393600174 1.9700536535856412 chr14 107349540 44342057 0.4130623848038846 2.0617476282139897 chr15 102531392 44048741 0.4296122401225178 2.1212549676649144 chr16 90354753 45652111 0.5052541176223457 3.125464063632852 chr17 81195210 41876021 0.5157449682068683 2.631588896222529 chr18 78077248 41784000 0.5351623049009104 4.645318443790692 chr19 59128983 29431104 0.49774412659862594 3.0118814082899106 chr20 63025520 32050155 0.508526625405074 2.521593192042548 chr21 48129895 21066966 0.4377106162396573 3.0472501932808433 chr22 51304566 19155867 0.3733754808490145 2.6265774717510633 chrMT 16571 1604058 96.79910687345362 69.41263889978536 chrX 155270560 38886161 0.2504413006560935 1.5681768721347435 chrY 59373566 11500848 0.19370317086900254 3.0273420634482013