BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238521.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 = 1,337,528 number of mapped reads = 1,140,540 (85.27%) number of supplementary alignments = 7,288 (0.54%) number of secondary alignments = 0 number of mapped bases = 69,488,486 bp number of sequenced bases = 69,446,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,024 duplication rate = 12.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8732 >>>>>>> ACTG content number of A's = 16,699,743 bp (24.05%) number of C's = 12,106,469 bp (17.43%) number of T's = 23,649,484 bp (34.05%) number of G's = 16,987,032 bp (24.46%) number of N's = 4,031 bp (0.01%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 485,471 number of insertions = 4,442 mapped reads with insertion percentage = 0.39% number of deletions = 24,922 mapped reads with deletion percentage = 2.16% homopolymer indels = 39.81% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.4259X There is a 1.68% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 5670648 0.022750787850594763 0.5374910747003265 chr2 243199373 7228910 0.02972421314589491 1.1175084827171085 chr3 198022430 5083024 0.025668930534788408 0.21253992603277247 chr4 191154276 3096680 0.016199899185095918 0.16791027237261427 chr5 180915260 5668840 0.03133422796949246 0.23340367572543472 chr6 171115067 3739831 0.02185564991772466 0.3666439066999186 chr7 159138663 6146967 0.03862648387337526 0.511093715837091 chr8 146364022 3292542 0.022495569300493807 0.22984414229008807 chr9 141213431 3524707 0.02496013994589509 0.2558822979827363 chr10 135534747 5225442 0.038554260923215504 0.2973843197667329 chr11 135006516 1547826 0.011464824408919641 0.14433947553632515 chr12 133851895 1412413 0.010552058302947448 0.1415664180867845 chr13 115169878 953516 0.008279213424190655 0.18306556447955724 chr14 107349540 694868 0.006472948090881433 0.11516904839299472 chr15 102531392 1207127 0.011773243066864829 0.21941953916302465 chr16 90354753 2058634 0.022783903797512457 0.21157620558524987 chr17 81195210 1951632 0.024036294751870215 0.20598345555313408 chr18 78077248 2801116 0.03587621325997556 0.5415717394363236 chr19 59128983 1516560 0.02564833560556927 0.38888875543105383 chr20 63025520 1555839 0.024685857411410488 0.20745299351092103 chr21 48129895 927561 0.01927203456396487 0.1873327805318148 chr22 51304566 449469 0.008760799185008212 0.11825976660682144 chrMT 16571 4947 0.2985335827650715 0.5681671070988326 chrX 155270560 3542698 0.022816289192233222 0.20566732175729038 chrY 59373566 186689 0.003144311729566656 0.14127488876434788