BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818953.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 = 2,622,875 number of mapped reads = 2,566,299 (97.84%) number of supplementary alignments = 28,491 (1.09%) number of secondary alignments = 0 number of mapped bases = 237,858,421 bp number of sequenced bases = 237,724,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,239,371 duplication rate = 39.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2772 >>>>>>> ACTG content number of A's = 68,234,299 bp (28.7%) number of C's = 51,212,156 bp (21.54%) number of T's = 66,494,186 bp (27.97%) number of G's = 51,774,050 bp (21.78%) number of N's = 10,194 bp (0%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,547,052 number of insertions = 28,008 mapped reads with insertion percentage = 1.06% number of deletions = 71,928 mapped reads with deletion percentage = 2.74% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0768X std coverageData = 0.921X There is a 3.19% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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% 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 27840296 0.1116959945307418 1.6711655948870878 chr2 243199373 20754780 0.0853405983082037 1.3411036068380413 chr3 198022430 15854642 0.08006487951895147 0.5663384344105492 chr4 191154276 15653630 0.08189003315834797 0.6431570813822516 chr5 180915260 11568965 0.06394687214334491 0.5226464453839399 chr6 171115067 12878772 0.07526381063801939 0.6212336316635282 chr7 159138663 11632565 0.07309703864987228 0.7408673108282983 chr8 146364022 14577061 0.0995945642980486 0.7383345000270445 chr9 141213431 8873805 0.0628396671418599 0.965979695185657 chr10 135534747 13144914 0.09698556488986547 1.1046756907554762 chr11 135006516 9039712 0.06695759780957536 0.6462115550735869 chr12 133851895 10211057 0.07628623412466443 0.5645580008379678 chr13 115169878 3725699 0.032349595785800864 0.3569852358649255 chr14 107349540 5576931 0.05195114017256152 0.499798746687229 chr15 102531392 7156459 0.06979773570225205 0.539299163159249 chr16 90354753 7562612 0.08369910545823749 0.9804819868645607 chr17 81195210 4809289 0.059231191101051406 0.5603841375173098 chr18 78077248 5832666 0.0747037856662161 1.2670235722385021 chr19 59128983 4107199 0.06946168852591292 1.4024797158678435 chr20 63025520 5522589 0.08762464792039797 0.6261156177567789 chr21 48129895 3306958 0.06870902170054599 0.5941618788163596 chr22 51304566 2971306 0.05791504015451568 0.5582629571118288 chrMT 16571 876837 52.91394605032889 34.52206998409308 chrX 155270560 13641573 0.08785679010882681 0.742513844367455 chrY 59373566 738104 0.012431525504127544 0.7690444541423798