BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672003.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 136,722,800 number of mapped reads = 103,652,859 (75.81%) number of supplementary alignments = 2,666,357 (1.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,834,238 number of mapped paired reads (second in pair) = 51,818,621 number of mapped paired reads (both in pair) = 102,811,590 number of mapped paired reads (singletons) = 841,269 number of mapped bases = 13,860,244,294 bp number of sequenced bases = 13,849,933,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,076,003 duplication rate = 28.53% >>>>>>> Insert size mean insert size = 202,135.305 std insert size = 4,379,678.2366 median insert size = 289 >>>>>>> Mapping quality mean mapping quality = 52.9292 >>>>>>> ACTG content number of A's = 3,750,753,298 bp (27.08%) number of C's = 2,780,731,446 bp (20.08%) number of T's = 4,104,901,690 bp (29.64%) number of G's = 3,213,498,062 bp (23.2%) number of N's = 48,975 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 177,400,554 number of insertions = 3,180,506 mapped reads with insertion percentage = 2.83% number of deletions = 4,366,444 mapped reads with deletion percentage = 4.02% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 4.4773X std coverageData = 99.4916X There is a 60.61% of reference with a coverageData >= 1X There is a 49.07% of reference with a coverageData >= 2X There is a 39.96% of reference with a coverageData >= 3X There is a 33.25% of reference with a coverageData >= 4X There is a 27.84% of reference with a coverageData >= 5X There is a 23.56% of reference with a coverageData >= 6X There is a 20.06% of reference with a coverageData >= 7X There is a 17.18% of reference with a coverageData >= 8X There is a 14.79% of reference with a coverageData >= 9X There is a 12.8% of reference with a coverageData >= 10X There is a 11.12% of reference with a coverageData >= 11X There is a 9.71% of reference with a coverageData >= 12X There is a 8.5% of reference with a coverageData >= 13X There is a 7.47% of reference with a coverageData >= 14X There is a 6.58% of reference with a coverageData >= 15X There is a 5.82% of reference with a coverageData >= 16X There is a 5.16% of reference with a coverageData >= 17X There is a 4.59% of reference with a coverageData >= 18X There is a 4.09% of reference with a coverageData >= 19X There is a 3.66% of reference with a coverageData >= 20X There is a 3.27% of reference with a coverageData >= 21X There is a 2.94% of reference with a coverageData >= 22X There is a 2.65% of reference with a coverageData >= 23X There is a 2.39% of reference with a coverageData >= 24X There is a 2.16% of reference with a coverageData >= 25X There is a 1.95% of reference with a coverageData >= 26X There is a 1.77% of reference with a coverageData >= 27X There is a 1.61% of reference with a coverageData >= 28X There is a 1.47% of reference with a coverageData >= 29X There is a 1.34% of reference with a coverageData >= 30X There is a 1.22% of reference with a coverageData >= 31X There is a 1.12% of reference with a coverageData >= 32X There is a 1.03% of reference with a coverageData >= 33X There is a 0.95% of reference with a coverageData >= 34X There is a 0.87% of reference with a coverageData >= 35X There is a 0.8% of reference with a coverageData >= 36X There is a 0.74% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.63% of reference with a coverageData >= 39X There is a 0.59% of reference with a coverageData >= 40X There is a 0.55% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.48% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.42% of reference with a coverageData >= 45X There is a 0.39% of reference with a coverageData >= 46X There is a 0.37% of reference with a coverageData >= 47X There is a 0.34% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.3% of reference with a coverageData >= 50X There is a 0.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1111396008 4.4589498053848375 109.11153395426423 chr2 243199373 1334148018 5.485820138195833 157.06965270546777 chr3 198022430 861630542 4.3511764904612065 7.662966910056131 chr4 191154276 940174862 4.9184087412201025 142.78998545413424 chr5 180915260 769493781 4.253338170588816 9.318627820272257 chr6 171115067 771975859 4.511442928634683 71.79706595821457 chr7 159138663 759293467 4.7712696128407215 126.00776808212808 chr8 146364022 680930411 4.652307320442452 33.74429398730518 chr9 141213431 650335816 4.60533967197497 224.31683004637583 chr10 135534747 678524514 5.006277202111131 64.95744964785433 chr11 135006516 628179536 4.65295716541563 42.37303741345555 chr12 133851895 590970178 4.4151050532381335 9.514053771253616 chr13 115169878 387959894 3.368588217137818 6.901430816268557 chr14 107349540 395980540 3.6887027182417365 11.170851785982617 chr15 102531392 384011838 3.7453099046972853 7.267626795776571 chr16 90354753 451371722 4.9955503945652975 50.63099817933302 chr17 81195210 415791441 5.120886330609896 71.65586968714638 chr18 78077248 447561156 5.7322865170657655 221.0177834720127 chr19 59128983 299181429 5.059810161118448 69.53098138801664 chr20 63025520 309355852 4.908422048719313 40.7034303451987 chr21 48129895 192441303 3.998373630360091 57.70692196994695 chr22 51304566 175712443 3.4248889855144666 11.312968493144723 chrMT 16571 4180002 252.2480236557842 260.60098674829874 chrX 155270560 403502708 2.5987071084177193 22.5148011846315 chrY 59373566 216140974 3.640356956157897 137.1639694146417