BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716909.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 733,513 number of mapped reads = 595,380 (81.17%) number of supplementary alignments = 1,013 (0.14%) number of secondary alignments = 0 number of mapped bases = 34,175,391 bp number of sequenced bases = 34,164,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,847 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7105 >>>>>>> ACTG content number of A's = 8,516,310 bp (24.93%) number of C's = 6,277,479 bp (18.37%) number of T's = 11,146,094 bp (32.62%) number of G's = 8,224,744 bp (24.07%) number of N's = 360 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 168,703 number of insertions = 2,279 mapped reads with insertion percentage = 0.38% number of deletions = 6,576 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.1313X There is a 1.04% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 3923266 0.015740245638144267 0.1649506142638932 chr2 243199373 3440297 0.014145994529352673 0.18205956989635044 chr3 198022430 2118249 0.010697015484558996 0.10897979385958512 chr4 191154276 1439817 0.007532224913451583 0.09267034507741509 chr5 180915260 2398897 0.0132597825081201 0.12006158292536448 chr6 171115067 1287037 0.007521470917578521 0.0979074134110657 chr7 159138663 2276325 0.01430403496603462 0.20216907427136152 chr8 146364022 1488800 0.01017189866509681 0.1146204975585729 chr9 141213431 943947 0.0066845412176126506 0.10341787543998127 chr10 135534747 1955032 0.014424581469134258 0.15744460124995685 chr11 135006516 1519541 0.01125531600267353 0.12860172372020856 chr12 133851895 1384913 0.010346607345379757 0.10598752564704082 chr13 115169878 986844 0.008568594645902117 0.0963771548023153 chr14 107349540 727184 0.006773983381763909 0.08864629947885609 chr15 102531392 1418442 0.013834221620633025 0.12327643102508677 chr16 90354753 1005318 0.011126343292643387 0.11509388241803609 chr17 81195210 1228649 0.015132037961352646 0.13133108913932606 chr18 78077248 1086934 0.013921264233083624 0.18086660858543444 chr19 59128983 518411 0.008767460113426946 0.13220770051562986 chr20 63025520 847343 0.013444442822526494 0.12097770587342463 chr21 48129895 416035 0.0086440038982009 0.0982552100775474 chr22 51304566 434914 0.008477101238903375 0.09577278228702275 chrMT 16571 6060 0.3656991129080924 0.6558388534187789 chrX 155270560 1253135 0.008070654218030772 0.10198153607902566 chrY 59373566 70001 0.0011789926850612274 0.040130910999787994