BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251074.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,450,496 number of mapped reads = 479,606 (33.06%) number of supplementary alignments = 19,383 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 240,425 number of mapped paired reads (second in pair) = 239,181 number of mapped paired reads (both in pair) = 468,348 number of mapped paired reads (singletons) = 11,258 number of mapped bases = 56,726,471 bp number of sequenced bases = 56,670,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,005 duplication rate = 49.28% >>>>>>> Insert size mean insert size = 108,342.2673 std insert size = 3,086,438.9539 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.0638 >>>>>>> ACTG content number of A's = 17,003,568 bp (30%) number of C's = 11,279,686 bp (19.9%) number of T's = 16,917,258 bp (29.85%) number of G's = 11,468,658 bp (20.24%) number of N's = 1,323 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 468,516 number of insertions = 13,381 mapped reads with insertion percentage = 2.49% number of deletions = 25,306 mapped reads with deletion percentage = 4.96% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 0.4084X There is a 0.52% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% 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% 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 4676782 0.01876337150630409 0.5307060363065118 chr2 243199373 5054434 0.020783088120872747 0.586308833016808 chr3 198022430 3729427 0.018833356403110495 0.3388314030700165 chr4 191154276 3635560 0.019018983389102948 0.35407694418744584 chr5 180915260 3363003 0.018588829930653722 0.33622536013270454 chr6 171115067 3135057 0.018321338120388896 0.34669721524090885 chr7 159138663 2930663 0.01841578246764584 0.4157593581862133 chr8 146364022 2900161 0.019814712388813695 0.40842665572811654 chr9 141213431 2379454 0.016850054439934967 0.46982794510860953 chr10 135534747 2755357 0.020329524797061817 0.480275183888534 chr11 135006516 2497018 0.01849553691171469 0.36846426926717407 chr12 133851895 2676496 0.01999595149549433 0.3768058271108719 chr13 115169878 2163426 0.018784651313080318 0.34364215215433747 chr14 107349540 1900400 0.017702917031596037 0.3379187410068192 chr15 102531392 1726125 0.016835087930923632 0.31878303725676593 chr16 90354753 1476920 0.016345792013841263 0.4229975007741427 chr17 81195210 1264286 0.015570943162780168 0.30428411865708277 chr18 78077248 1626104 0.020826861110678493 0.4488484237785814 chr19 59128983 987732 0.016704701313736445 0.38131969122141424 chr20 63025520 1160621 0.018415095980168033 0.33990668937020285 chr21 48129895 782632 0.016260829158260163 0.3254447147217136 chr22 51304566 570534 0.011120530675573788 0.2634648581981896 chrMT 16571 21731 1.3113873634662965 2.4969822348523745 chrX 155270560 3113228 0.02005034309143987 0.3525885823127812 chrY 59373566 199320 0.003357049499098639 0.23740082173216173