BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716900.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 = 1,215,443 number of mapped reads = 1,017,549 (83.72%) number of supplementary alignments = 3,487 (0.29%) number of secondary alignments = 0 number of mapped bases = 56,818,168 bp number of sequenced bases = 56,801,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,936 duplication rate = 1.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.3399 >>>>>>> ACTG content number of A's = 12,472,529 bp (21.96%) number of C's = 12,257,294 bp (21.58%) number of T's = 17,481,857 bp (30.78%) number of G's = 14,588,623 bp (25.68%) number of N's = 1,690 bp (0%) GC percentage = 47.26% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 297,636 number of insertions = 4,295 mapped reads with insertion percentage = 0.42% number of deletions = 9,662 mapped reads with deletion percentage = 0.94% homopolymer indels = 36.81% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1665X There is a 1.67% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4611731 0.01850238519566216 0.17447033276646542 chr2 243199373 4614835 0.0189755217831092 0.21275140236119366 chr3 198022430 3602438 0.018192070463936838 0.15232322428575878 chr4 191154276 3538797 0.01851277969842537 0.16836189961523124 chr5 180915260 3305299 0.018269873973041303 0.14811879342560363 chr6 171115067 3205359 0.018732184466257434 0.15232542617465386 chr7 159138663 3142761 0.01974856983685982 0.18454999196336141 chr8 146364022 2749046 0.018782252376202124 0.15490713192781477 chr9 141213431 2370608 0.016787411673327306 0.1488188549604843 chr10 135534747 2792285 0.020601986293595987 0.20484666360215872 chr11 135006516 2513239 0.018615686668042006 0.17047187190566834 chr12 133851895 2591565 0.019361436758142274 0.15285419099290481 chr13 115169878 1635667 0.014202211797081178 0.13029255524435607 chr14 107349540 1720033 0.016022732840774167 0.14126134740399413 chr15 102531392 1687596 0.016459310334926498 0.14165707122960908 chr16 90354753 1927331 0.02133070963073741 0.16919609791338727 chr17 81195210 1853211 0.022824141966010063 0.1695683227818557 chr18 78077248 1437826 0.018415428781506232 0.18512786486466987 chr19 59128983 1499365 0.02535753067154901 0.19692533139679286 chr20 63025520 1337474 0.02122114978186614 0.16502773977201035 chr21 48129895 733109 0.015231884465985225 0.15181117260111218 chr22 51304566 847758 0.016524026341047306 0.14628665614687078 chrMT 16571 4769 0.2877919256532497 0.6099023888525149 chrX 155270560 2895662 0.018649137350956937 0.15659807588721367 chrY 59373566 200404 0.0033753067821461155 0.10618286216208725