BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004067.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 = 3,035,174 number of mapped reads = 2,670,409 (87.98%) number of supplementary alignments = 28,402 (0.94%) number of secondary alignments = 0 number of mapped bases = 174,750,249 bp number of sequenced bases = 174,647,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,079 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1076 >>>>>>> ACTG content number of A's = 49,300,657 bp (28.23%) number of C's = 31,166,182 bp (17.85%) number of T's = 56,305,091 bp (32.24%) number of G's = 37,742,904 bp (21.61%) number of N's = 132,709 bp (0.08%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,577,634 number of insertions = 13,173 mapped reads with insertion percentage = 0.49% number of deletions = 60,542 mapped reads with deletion percentage = 2.24% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.0564X std coverageData = 0.5007X There is a 4.47% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13147343 0.05274748342552776 0.9308976199591544 chr2 243199373 12927945 0.053157805632993965 0.4807918092559078 chr3 198022430 9231755 0.04661974403606702 0.2591633667667203 chr4 191154276 10714377 0.056050940759494176 0.31869998533168425 chr5 180915260 11823493 0.06535376286113179 0.31358672162165385 chr6 171115067 11156959 0.06520149976039223 0.38602676055211443 chr7 159138663 10811625 0.06793839282161118 0.6548434484945451 chr8 146364022 14271665 0.09750801327391782 0.8143677581035551 chr9 141213431 7228076 0.05118547116102575 0.48487142552379425 chr10 135534747 8383714 0.06185656582957284 0.49253866231293775 chr11 135006516 7451483 0.055193506363796545 0.38077640685758485 chr12 133851895 8784931 0.06563172676785786 0.32512136939029634 chr13 115169878 7297624 0.06336399870111871 0.3034185721639712 chr14 107349540 4091046 0.038109581093687034 0.27421576517228297 chr15 102531392 4254335 0.0414929995293539 0.24736120570357142 chr16 90354753 3225442 0.03569753546888673 0.3005585337895273 chr17 81195210 4200648 0.0517351700919303 0.3262186247217496 chr18 78077248 4444995 0.056930733521755275 0.8594703710697561 chr19 59128983 2475409 0.04186456242617939 0.6576632237238704 chr20 63025520 3383587 0.05368598307479256 0.2979345975576106 chr21 48129895 1711454 0.03555906365472021 0.27161199405022696 chr22 51304566 1170720 0.02281902160521151 0.17592326721770174 chrMT 16571 181094 10.928368837125099 7.269210011350125 chrX 155270560 11914586 0.0767343532476472 0.37403475745523623 chrY 59373566 465943 0.007847650585784252 0.17537755149921175