BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008667.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 = 1,812,913 number of mapped reads = 1,514,017 (83.51%) number of supplementary alignments = 13,481 (0.74%) number of secondary alignments = 0 number of mapped bases = 99,625,999 bp number of sequenced bases = 99,578,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,285 duplication rate = 4.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2138 >>>>>>> ACTG content number of A's = 27,202,032 bp (27.32%) number of C's = 18,137,658 bp (18.21%) number of T's = 31,724,996 bp (31.86%) number of G's = 22,470,569 bp (22.57%) number of N's = 42,845 bp (0.04%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 850,834 number of insertions = 7,931 mapped reads with insertion percentage = 0.52% number of deletions = 29,264 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.3092X There is a 2.56% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 6494460 0.026055943106356394 0.5336898382642007 chr2 243199373 10809141 0.04444559567182766 0.36257627118838553 chr3 198022430 8736094 0.04411668920535921 0.2543680110141155 chr4 191154276 4858196 0.02541505270852534 0.22008817003003 chr5 180915260 4860802 0.026867838567072783 0.19756953985914502 chr6 171115067 4716308 0.027562201755149944 0.23698613402665056 chr7 159138663 7001362 0.04399535517022661 0.432569997589553 chr8 146364022 4454970 0.03043760303334654 0.3328001210418997 chr9 141213431 5536480 0.039206468965405986 0.29902275772038694 chr10 135534747 5397910 0.039826761177338535 0.3162508256623036 chr11 135006516 6074486 0.044994020881184725 0.32654171519785663 chr12 133851895 4284510 0.032009333898485336 0.22195957958426948 chr13 115169878 1919231 0.016664348641577967 0.15526314007856673 chr14 107349540 3846313 0.03582980420782427 0.23780644700931772 chr15 102531392 3301205 0.03219701728032718 0.21851522021189138 chr16 90354753 2754324 0.030483443411106443 0.22158243892794519 chr17 81195210 1933330 0.023810887366385283 0.21078447374517253 chr18 78077248 2802029 0.03588790680737108 0.46368683201479066 chr19 59128983 1964560 0.0332249922174376 0.37225804460435385 chr20 63025520 1914910 0.030383089262889063 0.21632936846160628 chr21 48129895 1144563 0.02378070843495503 0.2045681913390858 chr22 51304566 1022889 0.01993758216373958 0.16817698451203805 chrMT 16571 54257 3.2742139882928005 2.9116103018417703 chrX 155270560 3451132 0.022226570188192792 0.19980955319950935 chrY 59373566 292537 0.004927057943597324 0.13772888600516028