BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063608.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,947,467 number of mapped reads = 4,661,636 (94.22%) number of supplementary alignments = 30,432 (0.62%) number of secondary alignments = 0 number of mapped bases = 298,386,321 bp number of sequenced bases = 298,260,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 510,345 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1186 >>>>>>> ACTG content number of A's = 77,683,752 bp (26.05%) number of C's = 53,397,141 bp (17.9%) number of T's = 97,455,598 bp (32.67%) number of G's = 69,691,061 bp (23.37%) number of N's = 33,138 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,688,504 number of insertions = 19,248 mapped reads with insertion percentage = 0.41% number of deletions = 72,397 mapped reads with deletion percentage = 1.54% homopolymer indels = 44.41% >>>>>>> Coverage mean coverageData = 0.0964X std coverageData = 1.1673X There is a 7.3% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 36025690 0.1445360089995523 2.788713147555129 chr2 243199373 21338824 0.08774210121010469 1.6190011764125598 chr3 198022430 15159188 0.07655288342840758 0.36049764365053105 chr4 191154276 13345704 0.06981640316536786 0.3896206114486759 chr5 180915260 17700247 0.09783722500799545 0.40763268953677084 chr6 171115067 14256927 0.08331777703713256 0.5207818764181399 chr7 159138663 19953863 0.12538664472756064 1.591502243578179 chr8 146364022 12699091 0.0867637471727854 1.0983294235638963 chr9 141213431 10150411 0.07187992620900203 0.859865563299895 chr10 135534747 13224562 0.0975732223117663 0.7637223339900909 chr11 135006516 13806284 0.1022638344359616 0.8368187597311402 chr12 133851895 23042098 0.17214622176249353 0.5640702789039566 chr13 115169878 9325630 0.08097282173034863 0.4057677000038059 chr14 107349540 7825712 0.07289935289895047 0.43409224698082644 chr15 102531392 8061389 0.07862361802324892 0.41243805287268825 chr16 90354753 7970441 0.08821274736925018 0.46043641398014784 chr17 81195210 7414355 0.09131517733620001 0.48617435770562534 chr18 78077248 8753702 0.112115913716631 1.6271394711661478 chr19 59128983 4838112 0.08182302070035603 1.916970451715356 chr20 63025520 5751424 0.09125547873305924 0.4328998519776049 chr21 48129895 4912465 0.1020668131521999 0.44111630116175893 chr22 51304566 4351419 0.08481543338657226 0.365977948813152 chrMT 16571 262611 15.847625369621628 9.272860694943814 chrX 155270560 17454924 0.11241618501279316 0.559525076393531 chrY 59373566 761248 0.012821328602698379 0.34414162940331944