BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240259.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 = 1,409,053 number of mapped reads = 1,159,252 (82.27%) number of supplementary alignments = 7,653 (0.54%) number of secondary alignments = 0 number of mapped bases = 72,507,514 bp number of sequenced bases = 72,473,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,625 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6575 >>>>>>> ACTG content number of A's = 20,052,243 bp (27.67%) number of C's = 12,896,968 bp (17.8%) number of T's = 23,323,864 bp (32.18%) number of G's = 16,181,497 bp (22.33%) number of N's = 18,949 bp (0.03%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 609,859 number of insertions = 5,157 mapped reads with insertion percentage = 0.44% number of deletions = 19,958 mapped reads with deletion percentage = 1.7% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.2289X There is a 1.96% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 6091254 0.02443827010565402 0.33917295693077476 chr2 243199373 7434820 0.03057088473661484 0.2701100840749735 chr3 198022430 4642208 0.023442839278358517 0.1781744601348314 chr4 191154276 4352841 0.022771350403900985 0.17845038447234843 chr5 180915260 4243779 0.023457274969507825 0.17893435913026673 chr6 171115067 4516982 0.02639733647768142 0.21440193442431033 chr7 159138663 4004268 0.02516213171905309 0.2851551163656702 chr8 146364022 4047402 0.027652984283255074 0.34509908487180174 chr9 141213431 2960231 0.02096281479061294 0.205333376208887 chr10 135534747 3128839 0.023085142882216025 0.20813984821327558 chr11 135006516 3004754 0.02225636279659272 0.2057190084092283 chr12 133851895 3182486 0.023776174405300724 0.18125970784642634 chr13 115169878 1918920 0.01666164828272198 0.15024992951078428 chr14 107349540 2422240 0.022564046385294245 0.18029828130476072 chr15 102531392 1899535 0.018526374829671677 0.16131314478249115 chr16 90354753 2197675 0.024322738174050458 0.18483465413467323 chr17 81195210 1823908 0.022463246292484494 0.18318093779170494 chr18 78077248 1560498 0.01998659071590228 0.32044869970262724 chr19 59128983 1261754 0.021339010684489533 0.2341269373083225 chr20 63025520 1399934 0.022212176908655415 0.1766647111573782 chr21 48129895 1086501 0.022574348022159615 0.17997374525633164 chr22 51304566 668123 0.013022681061174945 0.13132204313156343 chrMT 16571 24745 1.4932713777080442 1.7919664832312674 chrX 155270560 4471036 0.028795130255213866 0.2087396502592995 chrY 59373566 162781 0.002741640951799998 0.06333735435109031