BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004038.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 = 3,079,193 number of mapped reads = 2,664,442 (86.53%) number of supplementary alignments = 31,370 (1.02%) number of secondary alignments = 0 number of mapped bases = 175,040,685 bp number of sequenced bases = 174,941,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,082 duplication rate = 6.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5843 >>>>>>> ACTG content number of A's = 49,861,595 bp (28.5%) number of C's = 30,954,886 bp (17.69%) number of T's = 56,705,658 bp (32.41%) number of G's = 37,340,585 bp (21.34%) number of N's = 78,441 bp (0.04%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,493,615 number of insertions = 12,747 mapped reads with insertion percentage = 0.47% number of deletions = 59,059 mapped reads with deletion percentage = 2.19% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.5087X There is a 3.75% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 11790288 0.0473029433294772 0.7759977438361066 chr2 243199373 12620739 0.051894619810553544 0.5026107978537652 chr3 198022430 13069716 0.0660011898652087 0.36220276028027887 chr4 191154276 14124205 0.07388903505355016 0.4033748357615306 chr5 180915260 13811097 0.07634014399890866 0.3910515967245545 chr6 171115067 6288194 0.036748336135706855 0.285678288776184 chr7 159138663 12577994 0.0790379519526314 0.6229569518598987 chr8 146364022 12139544 0.08294076532004566 1.086731705660152 chr9 141213431 6140193 0.043481650127175225 0.4149329120694806 chr10 135534747 7177155 0.05295435420704331 0.4802546526967239 chr11 135006516 6194383 0.04588210394230157 0.3483937526638764 chr12 133851895 6119743 0.04572025670611537 0.3084378379584217 chr13 115169878 7532477 0.06540318641303067 0.36442536258455804 chr14 107349540 3327082 0.03099297863782183 0.28099951057755207 chr15 102531392 3724861 0.03632898107927765 0.27004436334448667 chr16 90354753 4402907 0.048729113342825474 0.3532703927200507 chr17 81195210 2692015 0.033154849898165174 0.2664651870962185 chr18 78077248 6115115 0.07832134401048561 0.7975990493803754 chr19 59128983 2311186 0.03908719350035159 0.5587818286252021 chr20 63025520 3520174 0.055853152818096545 0.35913376989482215 chr21 48129895 2610406 0.054236685951631516 0.3465713646140893 chr22 51304566 1620782 0.031591379215643305 0.24176395617774188 chrMT 16571 6902 0.41651077183030594 0.8937615499601939 chrX 155270560 14623581 0.09418128587930642 0.4742815191721328 chrY 59373566 499946 0.00842034652255854 0.1871268779526451