BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 651,458 number of mapped reads = 514,159 (78.92%) number of supplementary alignments = 14,897 (2.29%) number of secondary alignments = 0 number of mapped bases = 67,565,224 bp number of sequenced bases = 66,033,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,067 duplication rate = 44.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.8968 >>>>>>> ACTG content number of A's = 18,285,677 bp (27.69%) number of C's = 13,640,200 bp (20.66%) number of T's = 17,419,771 bp (26.38%) number of G's = 16,687,459 bp (25.27%) number of N's = 548 bp (0%) GC percentage = 45.93% >>>>>>> Mismatches and indels general error rate = 0.0461 number of mismatches = 2,814,707 number of insertions = 79,504 mapped reads with insertion percentage = 14.85% number of deletions = 251,712 mapped reads with deletion percentage = 45.3% homopolymer indels = 29.81% >>>>>>> Coverage mean coverageData = 0.0218X std coverageData = 4.7331X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3565994 0.01430686104489184 2.5745033691091415 chr2 243199373 8303879 0.034144327337554445 11.893456878173092 chr3 198022430 4348585 0.021960062807026455 3.730567345866489 chr4 191154276 2655608 0.013892485460278168 2.6667522936631074 chr5 180915260 3468490 0.01917190401738361 3.945338397082965 chr6 171115067 2557911 0.01494848492798124 2.653160422985387 chr7 159138663 3897451 0.024490912054476666 5.306829503731907 chr8 146364022 3449179 0.02356575716401125 3.743472891700366 chr9 141213431 2241957 0.015876372269433777 2.562611167220247 chr10 135534747 3885848 0.028670492888439893 4.506665065500803 chr11 135006516 3190321 0.023630866824235357 3.345578204020505 chr12 133851895 3180962 0.023764788686779517 3.7396093392544105 chr13 115169878 2056793 0.017858775538513637 2.7464387474537855 chr14 107349540 2416348 0.022509160262819943 3.5656912547939337 chr15 102531392 1935795 0.018880022617853466 2.261169491876554 chr16 90354753 1488079 0.01646929409457851 2.026996495287479 chr17 81195210 2166605 0.02668390167351005 5.275505769639364 chr18 78077248 1948679 0.024958346380241272 3.7812852761828553 chr19 59128983 1567245 0.02650552944568656 4.295156946826967 chr20 63025520 1430431 0.022696060262573002 3.1201457246673954 chr21 48129895 792166 0.016458918100693967 3.0944476195338266 chr22 51304566 799896 0.015591126918411122 2.6056629602392576 chrMT 16571 452727 27.320439321706594 206.57565036902744 chrX 155270560 5421431 0.03491602657966842 3.3537437852632057 chrY 59373566 342844 0.005774354196613355 1.1582097920310752