BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819012.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,550,720 number of mapped reads = 2,486,071 (97.47%) number of supplementary alignments = 37,142 (1.46%) number of secondary alignments = 0 number of mapped bases = 230,192,495 bp number of sequenced bases = 230,052,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,153,325 duplication rate = 38.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1632 >>>>>>> ACTG content number of A's = 66,966,802 bp (29.11%) number of C's = 47,487,695 bp (20.64%) number of T's = 64,575,448 bp (28.07%) number of G's = 51,011,749 bp (22.17%) number of N's = 10,662 bp (0%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,443,263 number of insertions = 35,814 mapped reads with insertion percentage = 1.4% number of deletions = 74,922 mapped reads with deletion percentage = 2.94% homopolymer indels = 40.39% >>>>>>> Coverage mean coverageData = 0.0744X std coverageData = 0.8806X There is a 3.31% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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% 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 23178992 0.09299472116460644 1.6680602555859314 chr2 243199373 18467915 0.0759373462693919 1.1985083988618164 chr3 198022430 12296988 0.06209896525358264 0.4688196779358791 chr4 191154276 12684101 0.06635530873502406 0.5679339950479353 chr5 180915260 12467714 0.0689146620356956 0.520713144922304 chr6 171115067 9704075 0.05671081553560681 0.5581540927277314 chr7 159138663 11330423 0.07119843026455488 1.0185552443832533 chr8 146364022 21025333 0.1436509649891966 0.8249964055075698 chr9 141213431 9630544 0.06819849876744373 0.780644837907484 chr10 135534747 12282153 0.09061995740472367 1.0920268851186279 chr11 135006516 7850159 0.05814651938725683 0.551270832066394 chr12 133851895 10673851 0.0797437421412674 0.5478762678944786 chr13 115169878 4950084 0.04298071757964352 0.38763973804147744 chr14 107349540 5415499 0.050447342391965536 0.4579484314441583 chr15 102531392 5959480 0.05812346720114753 0.4592194118497196 chr16 90354753 7496986 0.08297279059575316 0.9845278163553937 chr17 81195210 8216812 0.10119823570873208 0.7035042831604063 chr18 78077248 5360241 0.06865304730002779 0.9301228514607955 chr19 59128983 4891668 0.08272876940907305 1.5150606729400868 chr20 63025520 6735317 0.10686650423510984 0.6781484119727285 chr21 48129895 3204686 0.06658410536736056 0.5576715049810508 chr22 51304566 1896049 0.03695673012807476 0.40275190644149966 chrMT 16571 45942 2.7724337698388752 3.798418520059299 chrX 155270560 13562054 0.08734465825330957 0.660947922683664 chrY 59373566 865429 0.01457599834916434 0.8405321352572153