BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237592.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 = 1,238,000 number of mapped reads = 951,710 (76.87%) number of supplementary alignments = 4,638 (0.37%) number of secondary alignments = 0 number of mapped bases = 59,269,854 bp number of sequenced bases = 59,234,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,106 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1909 >>>>>>> ACTG content number of A's = 16,126,904 bp (27.23%) number of C's = 10,366,209 bp (17.5%) number of T's = 18,488,372 bp (31.21%) number of G's = 14,141,978 bp (23.87%) number of N's = 110,724 bp (0.19%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 591,749 number of insertions = 5,672 mapped reads with insertion percentage = 0.59% number of deletions = 21,621 mapped reads with deletion percentage = 2.24% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.208X There is a 1.65% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.04% 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 4993370 0.02003353082919701 0.2524376538179419 chr2 243199373 5229084 0.021501223195998946 0.2883117139046723 chr3 198022430 4368136 0.02205879404671481 0.17499606509718615 chr4 191154276 3812681 0.019945570037889188 0.1701340020308811 chr5 180915260 3235581 0.017884511234707343 0.15285512417710576 chr6 171115067 3081289 0.01800711681338967 0.17562186419433953 chr7 159138663 3499781 0.02199202213983663 0.2878881349521401 chr8 146364022 3150424 0.02152457931225749 0.2257812641356631 chr9 141213431 2363006 0.016733578267070077 0.20357796358282296 chr10 135534747 2655124 0.019589987503352186 0.19728255243876294 chr11 135006516 2557664 0.018944744859574036 0.21031210716820045 chr12 133851895 3596587 0.02686989975001848 0.19797903188431962 chr13 115169878 2149992 0.018668006229892856 0.16430329350632292 chr14 107349540 1642478 0.015300279814892546 0.15853749488305421 chr15 102531392 1760539 0.017170731477048513 0.15504293573578315 chr16 90354753 1445992 0.016003496794463043 0.16042700932044238 chr17 81195210 1249493 0.01538875261237701 0.15381377953883546 chr18 78077248 1488024 0.01905835615517596 0.35560433662295166 chr19 59128983 975815 0.01650315886542476 0.1936399115651432 chr20 63025520 1204357 0.01910903710116156 0.1662192445302728 chr21 48129895 711623 0.014785467535302124 0.1499236160300972 chr22 51304566 550741 0.010734736553467775 0.1206782232708856 chrMT 16571 49336 2.977249411622714 2.504692614633448 chrX 155270560 3297548 0.02123743226017862 0.1763461960246584 chrY 59373566 201189 0.0033885281540947027 0.0885450865532688