BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173881.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,181,378 number of mapped reads = 6,023,737 (97.45%) number of supplementary alignments = 580,261 (9.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,014,088 number of mapped paired reads (second in pair) = 3,009,649 number of mapped paired reads (both in pair) = 5,919,382 number of mapped paired reads (singletons) = 104,355 number of mapped bases = 711,883,418 bp number of sequenced bases = 711,486,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,619,098 duplication rate = 64.54% >>>>>>> Insert size mean insert size = 728,826.2612 std insert size = 7,855,048.0944 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.8208 >>>>>>> ACTG content number of A's = 214,920,067 bp (30.21%) number of C's = 138,693,571 bp (19.49%) number of T's = 214,554,793 bp (30.16%) number of G's = 143,309,984 bp (20.14%) number of N's = 7,752 bp (0%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 6,971,077 number of insertions = 71,570 mapped reads with insertion percentage = 1.15% number of deletions = 161,315 mapped reads with deletion percentage = 2.61% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.23X std coverageData = 3.3012X There is a 4.86% of reference with a coverageData >= 1X There is a 3.8% of reference with a coverageData >= 2X There is a 2.89% of reference with a coverageData >= 3X There is a 2.36% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 1.08% of reference with a coverageData >= 7X There is a 0.89% of reference with a coverageData >= 8X There is a 0.66% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 54573742 0.21895127795890226 1.9933693083466912 chr2 243199373 61075321 0.25113272393181707 10.044136233172964 chr3 198022430 62637881 0.3163171010475935 1.6630120918332183 chr4 191154276 35336247 0.18485721449411888 1.4229814062535482 chr5 180915260 43486142 0.24036746264521855 1.4185462741275856 chr6 171115067 39950013 0.23346870442449116 1.6145239897625006 chr7 159138663 39016215 0.2451711875950598 2.004819385214867 chr8 146364022 41689536 0.28483458865321426 2.0726697969282157 chr9 141213431 29079097 0.205923025834561 1.5709066479202538 chr10 135534747 36227651 0.2672941943072355 3.2071795419814535 chr11 135006516 24695209 0.18291864520079906 1.252826335546763 chr12 133851895 30956102 0.23127130176229482 1.3844249103242834 chr13 115169878 19419992 0.1686204095831377 1.1977234218970396 chr14 107349540 21824899 0.20330687024834945 1.3072624807075337 chr15 102531392 23704648 0.23119405225669812 1.378425894216233 chr16 90354753 23394789 0.2589215090876293 1.8659439770915254 chr17 81195210 27027727 0.33287341704024165 1.872834472028252 chr18 78077248 13621904 0.17446700990280806 2.308296960823105 chr19 59128983 10883687 0.18406687292423074 1.6378616839677786 chr20 63025520 30541287 0.4845860375289248 2.244906665341418 chr21 48129895 8928491 0.1855082168785118 1.300712707865638 chr22 51304566 5031674 0.09807458462858842 0.8585015333399126 chrMT 16571 2386730 144.03053527246394 119.53023836480713 chrX 155270560 25262232 0.1626981444518523 1.1627768286529592 chrY 59373566 1132202 0.019069125812655418 0.7027192269647491