BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819029.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 = 745,564 number of mapped reads = 665,302 (89.23%) number of supplementary alignments = 3,199 (0.43%) number of secondary alignments = 0 number of mapped bases = 37,652,936 bp number of sequenced bases = 37,642,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,218 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7342 >>>>>>> ACTG content number of A's = 8,782,261 bp (23.33%) number of C's = 7,507,904 bp (19.95%) number of T's = 12,191,724 bp (32.39%) number of G's = 9,159,948 bp (24.33%) number of N's = 850 bp (0%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 189,186 number of insertions = 2,599 mapped reads with insertion percentage = 0.39% number of deletions = 6,096 mapped reads with deletion percentage = 0.91% homopolymer indels = 38.21% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.129X There is a 1.15% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4284610 0.01718996720172665 0.17599641077972303 chr2 243199373 3236286 0.013307131346921687 0.14838116105825905 chr3 198022430 2533249 0.012792737671181997 0.11764127204924597 chr4 191154276 2434029 0.012733322272110721 0.12272002522623332 chr5 180915260 1869785 0.010335142541320175 0.10572869667413541 chr6 171115067 2009564 0.011743933688784985 0.1159201800782533 chr7 159138663 1604086 0.0100798006578703 0.11657878758509503 chr8 146364022 2403200 0.01641933562060764 0.14163614028654714 chr9 141213431 1397776 0.00989832192378358 0.12118864882877846 chr10 135534747 1845864 0.01361912012127783 0.14442339949659105 chr11 135006516 1220995 0.009043970885079354 0.11915122269189445 chr12 133851895 1736071 0.012970089067472672 0.11910174107301764 chr13 115169878 1188430 0.010318930788482731 0.1055229121800109 chr14 107349540 658834 0.006137278278043856 0.08618192860245993 chr15 102531392 1106420 0.01079103656370919 0.10821155427365435 chr16 90354753 1154385 0.01277614028782747 0.12292425514794927 chr17 81195210 854151 0.010519721545150263 0.10893539784819473 chr18 78077248 919441 0.01177604261871525 0.1829583205785857 chr19 59128983 757475 0.012810553497935183 0.14187901297544298 chr20 63025520 1229233 0.019503734360303573 0.1474399323573379 chr21 48129895 502198 0.010434221807464986 0.11079267106277883 chr22 51304566 458187 0.00893072558103308 0.09853085538579959 chrMT 16571 1161 0.07006215677991673 0.2757096314161373 chrX 155270560 2137041 0.013763336720109723 0.12877911494005878 chrY 59373566 110465 0.0018605080921028055 0.056635083560521604