BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173955.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 = 3,893,586 number of mapped reads = 3,793,813 (97.44%) number of supplementary alignments = 499,600 (12.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,901,834 number of mapped paired reads (second in pair) = 1,891,979 number of mapped paired reads (both in pair) = 3,727,430 number of mapped paired reads (singletons) = 66,383 number of mapped bases = 428,768,742 bp number of sequenced bases = 428,453,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,023,102 duplication rate = 64.86% >>>>>>> Insert size mean insert size = 1,111,734.6212 std insert size = 9,733,645.0951 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.363 >>>>>>> ACTG content number of A's = 126,760,091 bp (29.59%) number of C's = 86,096,274 bp (20.09%) number of T's = 125,676,518 bp (29.33%) number of G's = 89,917,406 bp (20.99%) number of N's = 3,436 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 3,813,580 number of insertions = 49,130 mapped reads with insertion percentage = 1.24% number of deletions = 129,927 mapped reads with deletion percentage = 3.34% homopolymer indels = 40.64% >>>>>>> Coverage mean coverageData = 0.1385X std coverageData = 2.7633X There is a 3% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 1.71% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 35015207 0.1404819248173508 1.338900645255048 chr2 243199373 37435842 0.153930668234083 8.792006720857348 chr3 198022430 29397604 0.14845592996712545 1.1372379748905619 chr4 191154276 28696438 0.15012187328731272 1.5590324754496039 chr5 180915260 25485020 0.140867166208091 1.1100410633825115 chr6 171115067 26240817 0.1533518787097807 1.2805741469649212 chr7 159138663 23356963 0.1467711400842924 1.4361426860618478 chr8 146364022 21745712 0.1485727961206204 1.5894987221957362 chr9 141213431 19803501 0.14023808401057827 1.385403199901841 chr10 135534747 21259286 0.15685487648418306 1.772629065205159 chr11 135006516 19019981 0.1408819482461128 1.1246108655643354 chr12 133851895 20161200 0.15062319438959007 1.172991797439024 chr13 115169878 13361262 0.11601351179689537 1.0055421476812134 chr14 107349540 12686469 0.11817907184325149 1.024553628792842 chr15 102531392 12211500 0.11910010935967787 1.0416260682830634 chr16 90354753 14151120 0.1566173281443202 1.3981400602714824 chr17 81195210 12007705 0.14788686426206668 1.1991710246577134 chr18 78077248 11571647 0.14820766992197265 1.7528601422542807 chr19 59128983 8612784 0.1456609527682896 1.2654578471107492 chr20 63025520 9562087 0.1517177010201582 1.2369326874569497 chr21 48129895 6259392 0.13005206015928353 1.3165998490135828 chr22 51304566 5482824 0.10686814892849889 1.0760978896014362 chrMT 16571 632680 38.17995292981715 34.63959931817792 chrX 155270560 10947170 0.07050383536969275 0.7849440372364421 chrY 59373566 3664531 0.06171990747532328 1.083961901644681