BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008818.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 = 999,145 number of mapped reads = 749,363 (75%) number of supplementary alignments = 4,126 (0.41%) number of secondary alignments = 0 number of mapped bases = 46,309,509 bp number of sequenced bases = 46,283,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,140 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2982 >>>>>>> ACTG content number of A's = 13,337,290 bp (28.82%) number of C's = 8,799,187 bp (19.01%) number of T's = 13,674,783 bp (29.55%) number of G's = 10,465,164 bp (22.61%) number of N's = 7,410 bp (0.02%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 413,234 number of insertions = 3,538 mapped reads with insertion percentage = 0.47% number of deletions = 15,923 mapped reads with deletion percentage = 2.1% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1741X There is a 1.16% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 3940060 0.015807623604676996 0.22160208194808598 chr2 243199373 4008856 0.01648382539209918 0.19313230559202613 chr3 198022430 3213597 0.016228449474132805 0.15935420800724645 chr4 191154276 2673113 0.013984060707069926 0.15181244688141082 chr5 180915260 2379504 0.013152588676046455 0.14369736760820204 chr6 171115067 2806342 0.016400320843751297 0.17182261313234 chr7 159138663 2596906 0.016318510857414956 0.19663071134278745 chr8 146364022 3188754 0.02178646060983484 0.21342636220464864 chr9 141213431 1568929 0.011110338364344394 0.15383178745684767 chr10 135534747 2251778 0.016614027397712262 0.19189985231926943 chr11 135006516 1994726 0.014775035006458503 0.17416913019899669 chr12 133851895 2487886 0.018586856764336433 0.1780308807057305 chr13 115169878 1265253 0.010985971522866421 0.13040715510297043 chr14 107349540 1569174 0.014617426399777773 0.15424542214133483 chr15 102531392 1311429 0.012790512002411904 0.1435762121323914 chr16 90354753 1140071 0.012617720287498323 0.14266615609509392 chr17 81195210 1277186 0.015729819529994443 0.16799438297179797 chr18 78077248 1128243 0.01445034281946003 0.23699540339984604 chr19 59128983 819034 0.013851650382689653 0.17254058682247797 chr20 63025520 1056912 0.016769587938346243 0.16499057080496865 chr21 48129895 544870 0.011320822536596017 0.1417704785513593 chr22 51304566 489253 0.009536246734842276 0.1211331711279272 chrMT 16571 22207 1.3401122442821798 1.6280566371978502 chrX 155270560 2441347 0.015723180234553158 0.16263526162592887 chrY 59373566 134079 0.0022582271713307567 0.07128120070143479