BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525110.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 = 877,227 number of mapped reads = 805,112 (91.78%) number of supplementary alignments = 22,116 (2.52%) number of secondary alignments = 0 number of mapped bases = 61,936,891 bp number of sequenced bases = 61,913,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,249 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1884 >>>>>>> ACTG content number of A's = 15,876,286 bp (25.64%) number of C's = 11,565,069 bp (18.68%) number of T's = 19,638,129 bp (31.72%) number of G's = 14,831,494 bp (23.96%) number of N's = 2,233 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 456,729 number of insertions = 5,350 mapped reads with insertion percentage = 0.66% number of deletions = 13,914 mapped reads with deletion percentage = 1.7% homopolymer indels = 42.36% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.2343X There is a 1.84% of reference with a coverageData >= 1X There is a 0.11% 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 6090304 0.02443445868084718 0.39960076688433677 chr2 243199373 5316402 0.021860261950593103 0.32292543994056067 chr3 198022430 4096675 0.020687934190081397 0.15171242885690805 chr4 191154276 4078298 0.021335112587280027 0.1578117689196737 chr5 180915260 3788013 0.02093805132856123 0.15430100368883481 chr6 171115067 3594912 0.02100874027650645 0.16606871772185464 chr7 159138663 3371511 0.02118599551134849 0.290996059919795 chr8 146364022 1768230 0.01208104270324028 0.25397867975694755 chr9 141213431 2573714 0.018225702624561257 0.2180429584716027 chr10 135534747 2862979 0.02112357947589632 0.2411176681984746 chr11 135006516 3495579 0.025891928060716714 0.2874028053159458 chr12 133851895 2742693 0.020490505569607364 0.15175330502518986 chr13 115169878 2260068 0.019623776974045246 0.14798098669499307 chr14 107349540 1863353 0.017357810755407058 0.1492916646604025 chr15 102531392 1730586 0.016878596557042744 0.13678216756342956 chr16 90354753 1357550 0.015024666162277042 0.1379760501939867 chr17 81195210 1820584 0.02242230791693254 0.1813465835163268 chr18 78077248 1689596 0.021640055756063533 0.35232949716587053 chr19 59128983 1165386 0.019709217728300858 0.28674308270405086 chr20 63025520 1198783 0.019020596736052317 0.14692123266790352 chr21 48129895 781040 0.016227752003198842 0.14003999062553432 chr22 51304566 620314 0.012090814684993144 0.11518294843533458 chrMT 16571 3667 0.221290205781184 0.5143768542029603 chrX 155270560 3527993 0.022721583537793643 0.19009374205335822 chrY 59373566 138661 0.0023353995614816196 0.06180230460830162