BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716947.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,505,473 number of mapped reads = 3,236,425 (92.32%) number of supplementary alignments = 19,094 (0.54%) number of secondary alignments = 0 number of mapped bases = 189,838,019 bp number of sequenced bases = 189,781,475 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 220,389 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8058 >>>>>>> ACTG content number of A's = 48,698,847 bp (25.66%) number of C's = 39,781,534 bp (20.96%) number of T's = 56,643,513 bp (29.85%) number of G's = 44,654,921 bp (23.53%) number of N's = 2,660 bp (0%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 929,270 number of insertions = 10,829 mapped reads with insertion percentage = 0.33% number of deletions = 35,693 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0613X std coverageData = 0.5006X There is a 4.94% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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 21744855 0.0872409260717549 1.0457476731603628 chr2 243199373 16293280 0.06699556745978946 0.5949328686105357 chr3 198022430 17002495 0.08586146023963043 0.35241056917793673 chr4 191154276 8870406 0.04640443408129672 0.3119265223545459 chr5 180915260 8146048 0.04502687059123702 0.26066123685421877 chr6 171115067 13384008 0.07821642029921304 0.4817674079920189 chr7 159138663 10860329 0.06824444038467258 0.6313385268156538 chr8 146364022 12411273 0.08479729396886894 0.43536209415955185 chr9 141213431 7175213 0.050811122916488025 0.38594155234611804 chr10 135534747 9877160 0.07287548188657482 0.4668017285646603 chr11 135006516 6389421 0.04732676013948838 0.39600171464306183 chr12 133851895 8409361 0.06282586436299613 0.3134682343282253 chr13 115169878 4170385 0.03621072690551951 0.23025789542592362 chr14 107349540 4203980 0.03916160236923232 0.26815205077432264 chr15 102531392 5711172 0.055701691829171694 0.28864656362672453 chr16 90354753 4220015 0.04670495862016246 0.29766676178855855 chr17 81195210 4398416 0.05417088027729715 0.3020854891842179 chr18 78077248 3694320 0.047316216883054076 0.7524447998224374 chr19 59128983 4285796 0.07248215312615812 0.6706563761901917 chr20 63025520 3016947 0.047868657013857244 0.2711486623367879 chr21 48129895 1788597 0.03716187205478009 0.2848585565578358 chr22 51304566 3278429 0.06390131046035942 0.306913041927039 chrMT 16571 6437 0.3884497012853781 0.7379694806478324 chrX 155270560 10010062 0.06446851225370734 0.363159362427464 chrY 59373566 489614 0.00824632968819828 0.20587187029537685