BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716822.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 = 1,207,460 number of mapped reads = 957,273 (79.28%) number of supplementary alignments = 1,036 (0.09%) number of secondary alignments = 0 number of mapped bases = 50,583,381 bp number of sequenced bases = 50,570,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,556 duplication rate = 6.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1448 >>>>>>> ACTG content number of A's = 10,532,611 bp (20.83%) number of C's = 9,861,801 bp (19.5%) number of T's = 15,891,078 bp (31.42%) number of G's = 14,283,654 bp (28.25%) number of N's = 961 bp (0%) GC percentage = 47.75% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 328,287 number of insertions = 3,024 mapped reads with insertion percentage = 0.31% number of deletions = 7,792 mapped reads with deletion percentage = 0.81% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1682X There is a 1.4% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 4982582 0.019990249091495743 0.20106056909164147 chr2 243199373 4044199 0.016629150602292055 0.2305518870426782 chr3 198022430 3491688 0.017632790386422386 0.1530917310575668 chr4 191154276 3159420 0.016528115750860838 0.1566734302859874 chr5 180915260 3067633 0.016956187112131944 0.14885516523187406 chr6 171115067 2111635 0.01234043872945449 0.14565359635811664 chr7 159138663 3135139 0.019700674499194454 0.19071884069219158 chr8 146364022 3208002 0.021917968337874728 0.17640482055246806 chr9 141213431 2114194 0.01497162121923091 0.15106245663338394 chr10 135534747 2565016 0.018925154300099886 0.19518997306879146 chr11 135006516 2076147 0.015378124415861527 0.15960655761918358 chr12 133851895 2589610 0.019346831062795188 0.1605444944996986 chr13 115169878 871742 0.007569184018758794 0.09962595177344602 chr14 107349540 1648541 0.0153567588645466 0.14409933937070663 chr15 102531392 998678 0.009740216927904383 0.11310927524388205 chr16 90354753 1348450 0.01492395203603733 0.14923073853563318 chr17 81195210 2047266 0.025214122852813606 0.19008592588704853 chr18 78077248 1276098 0.016344044298282644 0.1754850129734051 chr19 59128983 1426888 0.024131786606240123 0.22522969392504233 chr20 63025520 1380070 0.021897002991803954 0.17524287622428242 chr21 48129895 665138 0.013819643695462042 0.1419333953688031 chr22 51304566 581880 0.011341680582582066 0.12412542266409468 chrMT 16571 73225 4.418864280972784 3.4694793136869198 chrX 155270560 1555188 0.010015987576782102 0.1186070429489897 chrY 59373566 164952 0.002778206045431059 0.09404946288197039