BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004100.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 = 5,050,987 number of mapped reads = 4,551,825 (90.12%) number of supplementary alignments = 30,626 (0.61%) number of secondary alignments = 0 number of mapped bases = 313,297,890 bp number of sequenced bases = 313,163,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 206,234 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1885 >>>>>>> ACTG content number of A's = 90,340,443 bp (28.85%) number of C's = 60,213,003 bp (19.23%) number of T's = 98,877,072 bp (31.57%) number of G's = 63,690,308 bp (20.34%) number of N's = 42,503 bp (0.01%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 3,071,180 number of insertions = 26,478 mapped reads with insertion percentage = 0.58% number of deletions = 79,547 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.1012X std coverageData = 0.7769X There is a 7.75% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.39% 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% 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 21843516 0.08763675658003676 1.4708256338289445 chr2 243199373 31876407 0.13107109038476017 0.8206299966451114 chr3 198022430 17923407 0.09051200411993732 0.3854606397599599 chr4 191154276 20836034 0.1090011400006558 0.47601047220490894 chr5 180915260 18634866 0.103003284521162 0.4063790662730982 chr6 171115067 19967019 0.11668767309660698 0.5033176900666055 chr7 159138663 18158273 0.1141034658560629 1.0797356826005156 chr8 146364022 18299264 0.12502569791365806 1.099690627392827 chr9 141213431 12717239 0.09005686576654312 0.7806427191010986 chr10 135534747 11270313 0.08315441795896074 0.7631206291113347 chr11 135006516 8415928 0.06233719859862171 0.43647566678644895 chr12 133851895 17345412 0.12958660017476778 0.459745120538349 chr13 115169878 8453238 0.07339799387475256 0.33234921264635653 chr14 107349540 10851192 0.10108279923695994 0.46585812291778167 chr15 102531392 9679009 0.09440044469502569 0.37927722594020297 chr16 90354753 8179296 0.09052424724131557 0.5404483994572884 chr17 81195210 8784888 0.10819465828095032 0.452545114736206 chr18 78077248 9793429 0.12543255879100657 1.6688047206351526 chr19 59128983 5727892 0.09687114016488327 0.9684215226124319 chr20 63025520 7122957 0.11301702865759775 0.43230295729971574 chr21 48129895 4703325 0.09772148889998618 0.4760941898825826 chr22 51304566 3632301 0.07079878621329727 0.3229624155830259 chrMT 16571 13759 0.8303059561885221 1.1070514269444123 chrX 155270560 18205258 0.11724861428979196 0.47611828549265767 chrY 59373566 863668 0.01454633868546821 0.3344313486614322