BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524411.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 = 1,124,488 number of mapped reads = 1,021,048 (90.8%) number of supplementary alignments = 3,739 (0.33%) number of secondary alignments = 0 number of mapped bases = 59,160,637 bp number of sequenced bases = 59,141,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,634 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5153 >>>>>>> ACTG content number of A's = 15,687,777 bp (26.53%) number of C's = 10,302,706 bp (17.42%) number of T's = 18,788,114 bp (31.77%) number of G's = 14,361,248 bp (24.28%) number of N's = 1,238 bp (0%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 304,561 number of insertions = 4,024 mapped reads with insertion percentage = 0.39% number of deletions = 12,188 mapped reads with deletion percentage = 1.18% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.2022X There is a 1.76% 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 4750671 0.01905981610372798 0.3294943152266722 chr2 243199373 5084325 0.02090599551011178 0.2782858406437811 chr3 198022430 3964414 0.020020025004238155 0.15151931685753423 chr4 191154276 3836051 0.020067827308241852 0.1595417033332584 chr5 180915260 3552261 0.01963494400638177 0.1492201814363998 chr6 171115067 3465660 0.020253388908178377 0.16315364095226995 chr7 159138663 3365790 0.02115004573087308 0.2798385065217332 chr8 146364022 2994709 0.020460690811024584 0.20103866668308154 chr9 141213431 2438894 0.017270977574364015 0.16987729716921166 chr10 135534747 2812607 0.020751925703598354 0.1981596961302841 chr11 135006516 2720342 0.020149708922197505 0.1726217906210549 chr12 133851895 2653367 0.019823156033764035 0.15111855244258948 chr13 115169878 1856064 0.016115880577732312 0.1352130128673679 chr14 107349540 1807641 0.016838833217170748 0.1405729834292826 chr15 102531392 1685074 0.01643471299014452 0.13826120234621977 chr16 90354753 1685484 0.018654071247364266 0.15492908603878547 chr17 81195210 1568941 0.019323073368490578 0.15187895817540353 chr18 78077248 1550370 0.019856873029131354 0.27157752911936317 chr19 59128983 1164694 0.01969751449978431 0.2564042686586754 chr20 63025520 1221240 0.019376912717261198 0.1492844467701147 chr21 48129895 768496 0.015967123967338803 0.1451016262575982 chr22 51304566 662738 0.012917719643121044 0.12097530228917243 chrMT 16571 12777 0.771045802908696 1.0298744943593867 chrX 155270560 3352936 0.021594151524925265 0.16515469269719676 chrY 59373566 185091 0.0031173973953324617 0.09180829012141101