BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717044.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 = 1,867,859 number of mapped reads = 1,710,095 (91.55%) number of supplementary alignments = 47,250 (2.53%) number of secondary alignments = 0 number of mapped bases = 130,250,153 bp number of sequenced bases = 130,202,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,207 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6884 >>>>>>> ACTG content number of A's = 33,742,257 bp (25.92%) number of C's = 26,936,923 bp (20.69%) number of T's = 38,924,719 bp (29.9%) number of G's = 30,583,752 bp (23.49%) number of N's = 15,001 bp (0.01%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 980,555 number of insertions = 9,450 mapped reads with insertion percentage = 0.54% number of deletions = 27,731 mapped reads with deletion percentage = 1.6% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.3631X There is a 3.67% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11404580 0.04575547276169073 0.5071173816549672 chr2 243199373 10588955 0.04354022327187496 0.5405997746328359 chr3 198022430 9806701 0.04952318280307943 0.2521808880217344 chr4 191154276 5700490 0.029821409801996792 0.20104055095825632 chr5 180915260 8207279 0.0453653218639489 0.23970029254200023 chr6 171115067 9361171 0.054706877448728694 0.3109334329590366 chr7 159138663 6962686 0.043752321835203556 0.5439803735663495 chr8 146364022 9908758 0.06769941044664651 0.4907259210266256 chr9 141213431 5760913 0.040795786627406565 0.33566216697720613 chr10 135534747 6531355 0.04818952441767571 0.3471072969179474 chr11 135006516 5423510 0.0401722091695189 0.3232468674040707 chr12 133851895 4517010 0.03374632835792127 0.20508065585306495 chr13 115169878 4849042 0.04210338748470325 0.22819984678102254 chr14 107349540 3089740 0.028782051604506177 0.21361503681465782 chr15 102531392 2924489 0.02852286449012611 0.1881129404938519 chr16 90354753 3266361 0.03615040594488704 0.24061860899553153 chr17 81195210 4175717 0.05142811995929317 0.2864637836543623 chr18 78077248 3566185 0.04567508578171198 0.6468888999064757 chr19 59128983 2355224 0.03983197208042628 0.46116124690312477 chr20 63025520 2573137 0.040826906307159384 0.2535441972536008 chr21 48129895 2835880 0.05892138347694297 0.2812795192299332 chr22 51304566 1885674 0.036754506411768494 0.21580237915937928 chrMT 16571 2946 0.1777804598394786 0.7393464685041675 chrX 155270560 4279839 0.02756375065562976 0.22999128614040598 chrY 59373566 272511 0.004589769797556037 0.12984699259488403