BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716672.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 = 1,134,139 number of mapped reads = 994,313 (87.67%) number of supplementary alignments = 3,667 (0.32%) number of secondary alignments = 0 number of mapped bases = 56,277,507 bp number of sequenced bases = 56,261,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,087 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6797 >>>>>>> ACTG content number of A's = 14,212,493 bp (25.26%) number of C's = 10,384,331 bp (18.46%) number of T's = 18,180,701 bp (32.31%) number of G's = 13,483,791 bp (23.97%) number of N's = 342 bp (0%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 289,204 number of insertions = 3,812 mapped reads with insertion percentage = 0.38% number of deletions = 10,221 mapped reads with deletion percentage = 1.02% homopolymer indels = 42.41% >>>>>>> Coverage mean coverageData = 0.0182X std coverageData = 0.1854X There is a 1.7% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 6739157 0.027037673859998126 0.2886458270699956 chr2 243199373 5812747 0.023901159482018895 0.2608265046777218 chr3 198022430 3724316 0.018807546195650664 0.14474828746454052 chr4 191154276 2449645 0.012815015448568882 0.12288903252786114 chr5 180915260 4165401 0.023024044516753314 0.15942474363388515 chr6 171115067 2156527 0.012602788508390089 0.1329540460475251 chr7 159138663 3027985 0.019027337184553322 0.24457748160101536 chr8 146364022 2568183 0.0175465456941324 0.1589639348173121 chr9 141213431 1571790 0.011130598476854514 0.140247199261089 chr10 135534747 2619264 0.019325405904952183 0.1847966059405501 chr11 135006516 2809134 0.020807395696367723 0.19506594893702042 chr12 133851895 2263940 0.016913768759119922 0.1376784301392917 chr13 115169878 1700035 0.01476110793483692 0.12745937662508872 chr14 107349540 1245701 0.01160415778213861 0.1161713981530656 chr15 102531392 2010500 0.01960862874074703 0.1527317025698066 chr16 90354753 1661278 0.018386171671566632 0.1510741894239469 chr17 81195210 2045749 0.025195439484669107 0.17649917750832342 chr18 78077248 1867863 0.023923268914396164 0.29240636021004457 chr19 59128983 854837 0.014457157160981443 0.21022431614191173 chr20 63025520 1322820 0.020988640791857013 0.15319754902614677 chr21 48129895 707585 0.014701569575416693 0.12992106186797797 chr22 51304566 622490 0.012133228063950487 0.11551357043052081 chrMT 16571 1762 0.10633033612938265 0.34642113170420374 chrX 155270560 2205596 0.014204856348814611 0.14556319418044794 chrY 59373566 123202 0.002075031167910649 0.05724749299233174