BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 371,336,068 number of mapped reads = 371,172,327 (99.96%) number of supplementary alignments = 172,036 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,592,133 number of mapped paired reads (second in pair) = 185,580,194 number of mapped paired reads (both in pair) = 371,111,790 number of mapped paired reads (singletons) = 60,537 number of mapped bases = 51,182,285,898 bp number of sequenced bases = 51,131,808,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 177,516,113 duplication rate = 31.72% >>>>>>> Insert size mean insert size = 75,597.9161 std insert size = 2,745,854.1444 median insert size = 309 >>>>>>> Mapping quality mean mapping quality = 55.384 >>>>>>> ACTG content number of A's = 14,036,159,068 bp (27.45%) number of C's = 11,056,213,173 bp (21.62%) number of T's = 13,849,067,242 bp (27.09%) number of G's = 12,188,436,595 bp (23.84%) number of N's = 1,931,926 bp (0%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 521,999,498 number of insertions = 10,611,113 mapped reads with insertion percentage = 2.79% number of deletions = 34,821,980 mapped reads with deletion percentage = 8.94% homopolymer indels = 51.83% >>>>>>> Coverage mean coverageData = 16.5334X std coverageData = 48.9405X There is a 58.94% of reference with a coverageData >= 1X There is a 50.94% of reference with a coverageData >= 2X There is a 45.55% of reference with a coverageData >= 3X There is a 41.48% of reference with a coverageData >= 4X There is a 38.22% of reference with a coverageData >= 5X There is a 35.52% of reference with a coverageData >= 6X There is a 33.22% of reference with a coverageData >= 7X There is a 31.23% of reference with a coverageData >= 8X There is a 29.48% of reference with a coverageData >= 9X There is a 27.93% of reference with a coverageData >= 10X There is a 26.54% of reference with a coverageData >= 11X There is a 25.29% of reference with a coverageData >= 12X There is a 24.16% of reference with a coverageData >= 13X There is a 23.12% of reference with a coverageData >= 14X There is a 22.16% of reference with a coverageData >= 15X There is a 21.29% of reference with a coverageData >= 16X There is a 20.47% of reference with a coverageData >= 17X There is a 19.72% of reference with a coverageData >= 18X There is a 19.01% of reference with a coverageData >= 19X There is a 18.35% of reference with a coverageData >= 20X There is a 17.73% of reference with a coverageData >= 21X There is a 17.15% of reference with a coverageData >= 22X There is a 16.61% of reference with a coverageData >= 23X There is a 16.09% of reference with a coverageData >= 24X There is a 15.61% of reference with a coverageData >= 25X There is a 15.15% of reference with a coverageData >= 26X There is a 14.71% of reference with a coverageData >= 27X There is a 14.29% of reference with a coverageData >= 28X There is a 13.9% of reference with a coverageData >= 29X There is a 13.52% of reference with a coverageData >= 30X There is a 13.16% of reference with a coverageData >= 31X There is a 12.82% of reference with a coverageData >= 32X There is a 12.49% of reference with a coverageData >= 33X There is a 12.17% of reference with a coverageData >= 34X There is a 11.87% of reference with a coverageData >= 35X There is a 11.59% of reference with a coverageData >= 36X There is a 11.31% of reference with a coverageData >= 37X There is a 11.04% of reference with a coverageData >= 38X There is a 10.79% of reference with a coverageData >= 39X There is a 10.54% of reference with a coverageData >= 40X There is a 10.31% of reference with a coverageData >= 41X There is a 10.08% of reference with a coverageData >= 42X There is a 9.86% of reference with a coverageData >= 43X There is a 9.64% of reference with a coverageData >= 44X There is a 9.44% of reference with a coverageData >= 45X There is a 9.24% of reference with a coverageData >= 46X There is a 9.05% of reference with a coverageData >= 47X There is a 8.86% of reference with a coverageData >= 48X There is a 8.68% of reference with a coverageData >= 49X There is a 8.51% of reference with a coverageData >= 50X There is a 8.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4226166618 16.95549082704191 49.97385351592951 chr2 243199373 3672577969 15.101099660318614 47.08939475601163 chr3 198022430 3687575883 18.622011067130124 49.6613672887392 chr4 191154276 2437962807 12.753901497866572 38.47136707868369 chr5 180915260 2752250230 15.212924714034626 42.915476793949715 chr6 171115067 2849339122 16.651596916360383 47.02743491090859 chr7 159138663 3633547847 22.832590009883393 60.26311972972432 chr8 146364022 3401029614 23.236787070527484 62.80207299993501 chr9 141213431 2074249674 14.68875629825891 48.2164959848858 chr10 135534747 2466229030 18.19628607858028 48.41901973897954 chr11 135006516 2937628533 21.75916111337915 57.53975436308106 chr12 133851895 2431568349 18.16611075248505 49.91465204284347 chr13 115169878 1023802518 8.88949902334706 30.243985052759115 chr14 107349540 1210802884 11.279069141796043 35.156962222213515 chr15 102531392 1807189718 17.625721086474666 51.10913873514334 chr16 90354753 1261392799 13.960447647950518 48.23634611214775 chr17 81195210 1797901510 22.14295042774075 57.96383768704588 chr18 78077248 1794369230 22.981973314428295 62.83299052438031 chr19 59128983 1421008378 24.03234938101337 65.18288528023197 chr20 63025520 1373916160 21.799362543934585 54.929849767354 chr21 48129895 619249786 12.866219342468959 47.83537204919994 chr22 51304566 942815721 18.376838447478534 55.440277217118556 chrMT 16571 3981899 240.29322310059743 452.0816863412122 chrX 155270560 1266286567 8.15535518774454 24.872031219675556 chrY 59373566 89443052 1.5064456798838728 14.891716524138152