BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173841.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 = 2,133,470 number of mapped reads = 2,081,173 (97.55%) number of supplementary alignments = 196,780 (9.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,040,513 number of mapped paired reads (second in pair) = 1,040,660 number of mapped paired reads (both in pair) = 2,046,540 number of mapped paired reads (singletons) = 34,633 number of mapped bases = 246,099,778 bp number of sequenced bases = 245,973,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,604,259 duplication rate = 64.73% >>>>>>> Insert size mean insert size = 864,818.108 std insert size = 8,678,904.4851 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.8423 >>>>>>> ACTG content number of A's = 74,111,948 bp (30.13%) number of C's = 48,262,696 bp (19.62%) number of T's = 73,848,687 bp (30.02%) number of G's = 49,746,390 bp (20.22%) number of N's = 3,399 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,504,413 number of insertions = 24,387 mapped reads with insertion percentage = 1.14% number of deletions = 49,719 mapped reads with deletion percentage = 2.33% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0795X std coverageData = 1.355X There is a 1.7% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.64% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 21019459 0.08433061837787759 1.0761030329674637 chr2 243199373 23623394 0.0971359165469559 3.6434570554755865 chr3 198022430 18108161 0.09144499943768997 0.8721175001743066 chr4 191154276 15186205 0.07944475696688051 0.8800853303556874 chr5 180915260 16665299 0.09211660199366267 0.8748834257983239 chr6 171115067 14245174 0.08324909226140793 0.8452091046441865 chr7 159138663 16217829 0.10191004935111211 1.2466994749785592 chr8 146364022 10199058 0.06968282136985823 0.8174610725255763 chr9 141213431 9991986 0.07075804283800738 0.8502875668800824 chr10 135534747 10211899 0.07534524707527583 1.427566162017056 chr11 135006516 11197238 0.08293850053874437 0.819377928421853 chr12 133851895 8591477 0.06418644278439241 0.7216234040959436 chr13 115169878 7929170 0.0688476026691632 0.7471701455775851 chr14 107349540 6291781 0.05861022785938347 0.6906556081109916 chr15 102531392 8256399 0.0805255721096618 0.800680798336382 chr16 90354753 10364970 0.11471416451108 1.139967115421136 chr17 81195210 5805624 0.07150205042883688 0.800605604161212 chr18 78077248 4294642 0.055005038087408 0.9553772308803449 chr19 59128983 4405318 0.07450353069661286 1.0591942842135444 chr20 63025520 7448549 0.11818306298781826 0.9712391014005339 chr21 48129895 4831855 0.10039197052060886 0.9225191355237568 chr22 51304566 2087278 0.040684059192704215 0.5539487161145046 chrMT 16571 581433 35.087381570213026 38.890307674313725 chrX 155270560 8196513 0.05278858400459173 0.6574883287894827 chrY 59373566 349067 0.005879165149015978 0.29613832700724235