BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083613.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,444,341 number of mapped reads = 1,327,303 (91.9%) number of supplementary alignments = 11,204 (0.78%) number of secondary alignments = 0 number of mapped bases = 89,098,467 bp number of sequenced bases = 89,065,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,314 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2457 >>>>>>> ACTG content number of A's = 24,647,856 bp (27.67%) number of C's = 16,240,650 bp (18.23%) number of T's = 28,463,893 bp (31.96%) number of G's = 19,708,780 bp (22.13%) number of N's = 4,298 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 608,878 number of insertions = 6,885 mapped reads with insertion percentage = 0.51% number of deletions = 20,172 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.27% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2451X There is a 2.54% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 8680244 0.03482536559056356 0.4158277599287707 chr2 243199373 7931044 0.03261128473386319 0.307672629650535 chr3 198022430 7718181 0.038976296776077335 0.22077697923264794 chr4 191154276 4314849 0.022572599945396985 0.16849275948976386 chr5 180915260 4257568 0.023533492973450663 0.16929398240434526 chr6 171115067 6039476 0.035294822985985214 0.23542682467837472 chr7 159138663 6280592 0.03946616040125962 0.3309228603164421 chr8 146364022 6132204 0.041896935573415714 0.31932386140824764 chr9 141213431 3489928 0.02471385317449018 0.19678851827744284 chr10 135534747 3966976 0.029269070019365587 0.21557341606598043 chr11 135006516 3334411 0.024698148643432883 0.1927505689001341 chr12 133851895 3196170 0.023878406801786406 0.17147615691271 chr13 115169878 2711658 0.023544854323801576 0.1698116219298918 chr14 107349540 1997433 0.01860681471015153 0.15302789885549986 chr15 102531392 2198907 0.021446183038264028 0.16749516296557418 chr16 90354753 2460424 0.02723070915815574 0.18790847793377524 chr17 81195210 1752097 0.021578822198994253 0.16676665495310491 chr18 78077248 2254480 0.02887499313500394 0.29898867224138576 chr19 59128983 2345292 0.039664000309289946 0.301763976206021 chr20 63025520 1844295 0.029262670105696865 0.19230989649168406 chr21 48129895 1378052 0.028631934476482858 0.19016886310102862 chr22 51304566 641826 0.012510114596817758 0.12223290639037641 chrMT 16571 2152 0.1298654275541609 0.40874290473237224 chrX 155270560 4005616 0.025797652819697436 0.18372550931309492 chrY 59373566 164592 0.002772142741097949 0.06450319990657431