BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818782.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,449,181 number of mapped reads = 1,409,232 (97.24%) number of supplementary alignments = 10,840 (0.75%) number of secondary alignments = 0 number of mapped bases = 95,731,534 bp number of sequenced bases = 95,691,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 504,399 duplication rate = 31.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7285 >>>>>>> ACTG content number of A's = 26,663,826 bp (27.86%) number of C's = 20,749,164 bp (21.68%) number of T's = 28,515,079 bp (29.8%) number of G's = 19,757,655 bp (20.65%) number of N's = 6,029 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 501,015 number of insertions = 12,190 mapped reads with insertion percentage = 0.85% number of deletions = 24,675 mapped reads with deletion percentage = 1.73% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.4055X There is a 1.76% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 7837087 0.03144259768965631 0.5579980376295857 chr2 243199373 8437720 0.034694661815596044 0.7171533961384783 chr3 198022430 6554640 0.03310049270681104 0.2854000678565711 chr4 191154276 6366617 0.033306170979926185 0.332912940769324 chr5 180915260 6017624 0.03326211398640446 0.2954787435287997 chr6 171115067 5611397 0.03279312043281379 0.3145632565930194 chr7 159138663 5292912 0.03325974907807287 0.3552563274697402 chr8 146364022 5012867 0.03424931162386341 0.3285566495466315 chr9 141213431 4106422 0.029079542724232795 0.31805750524230225 chr10 135534747 4586177 0.033837647551738154 0.40496853363047 chr11 135006516 4480845 0.033189842481380676 0.3282991660697465 chr12 133851895 4309482 0.03219589830984462 0.30543357298215607 chr13 115169878 3101498 0.0269297671740175 0.25841358416231647 chr14 107349540 2915452 0.02715849550915635 0.29101543884644504 chr15 102531392 2806016 0.02736738422511615 0.26056206232056994 chr16 90354753 2805661 0.03105161496042162 0.4780430395236366 chr17 81195210 2554166 0.031457101964512436 0.2943121384871046 chr18 78077248 2571821 0.032939442230340905 0.406694005084793 chr19 59128983 1849727 0.03128291585870841 0.47412969817896483 chr20 63025520 2031300 0.03222980151532268 0.29926333318576553 chr21 48129895 1294762 0.02690140919692428 0.2724279923529941 chr22 51304566 1135427 0.022131110123804577 0.26084867455667055 chrMT 16571 76632 4.624464425804115 4.580432059677086 chrX 155270560 3021811 0.019461583702667137 0.25379837530858407 chrY 59373566 953471 0.01605884679387457 0.7750713690681129