BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716123.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 = 888,388 number of mapped reads = 571,587 (64.34%) number of supplementary alignments = 1,925 (0.22%) number of secondary alignments = 0 number of mapped bases = 31,634,960 bp number of sequenced bases = 31,625,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,066 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9805 >>>>>>> ACTG content number of A's = 7,586,973 bp (23.99%) number of C's = 6,327,546 bp (20.01%) number of T's = 10,227,568 bp (32.34%) number of G's = 7,482,866 bp (23.66%) number of N's = 555 bp (0%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 168,207 number of insertions = 2,408 mapped reads with insertion percentage = 0.42% number of deletions = 6,065 mapped reads with deletion percentage = 1.05% homopolymer indels = 39.3% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1273X There is a 0.97% 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 2354411 0.009445958411473727 0.1469460880748298 chr2 243199373 3075220 0.012644851678955604 0.1708165863712697 chr3 198022430 2242232 0.011323121325195333 0.11211039337003939 chr4 191154276 1813701 0.009488152909537844 0.10263570661400782 chr5 180915260 1695537 0.009371995485621279 0.10037246966087171 chr6 171115067 1798365 0.010509682353103365 0.11182192533537595 chr7 159138663 1577092 0.00991017500253851 0.20877014743322517 chr8 146364022 2575553 0.01759689959872789 0.14568270841250572 chr9 141213431 1318049 0.00933373681714454 0.1079429348649948 chr10 135534747 1514893 0.011177155921499598 0.1433867399627283 chr11 135006516 1073295 0.007949949615765213 0.10103321891365306 chr12 133851895 1502247 0.011223203078297845 0.11133337221018183 chr13 115169878 837083 0.007268245955769789 0.08846184581220685 chr14 107349540 1013152 0.009437879286674167 0.10230227493133619 chr15 102531392 757975 0.0073926139615855405 0.0906501120768197 chr16 90354753 984613 0.010897190986732043 0.11188785113102112 chr17 81195210 1361448 0.016767590107840104 0.13840973187596128 chr18 78077248 717978 0.009195739071131196 0.14088127468625802 chr19 59128983 676710 0.011444641285306733 0.14569700296254162 chr20 63025520 683967 0.010852223036001925 0.1090912017926606 chr21 48129895 320414 0.006657276106669254 0.08550557461792711 chr22 51304566 466996 0.009102425698328682 0.09904187633010797 chrMT 16571 2289 0.13813288274696758 0.3732674321572277 chrX 155270560 1201957 0.007741048914874784 0.10256185566137746 chrY 59373566 69783 0.0011753210174372886 0.04145268452073843