BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716518.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 = 1,276,495 number of mapped reads = 1,166,915 (91.42%) number of supplementary alignments = 4,771 (0.37%) number of secondary alignments = 0 number of mapped bases = 67,802,334 bp number of sequenced bases = 67,781,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,115 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2366 >>>>>>> ACTG content number of A's = 16,863,580 bp (24.88%) number of C's = 12,196,189 bp (17.99%) number of T's = 21,149,085 bp (31.2%) number of G's = 17,570,777 bp (25.92%) number of N's = 1,918 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 343,862 number of insertions = 4,551 mapped reads with insertion percentage = 0.39% number of deletions = 12,981 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0219X std coverageData = 0.2168X There is a 2% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 5471314 0.021951054637492758 0.38670817446367445 chr2 243199373 5700817 0.023440919808621383 0.27354682921324214 chr3 198022430 4510693 0.02277869734251822 0.16296473218053045 chr4 191154276 4317458 0.022586248606858265 0.17049638732098885 chr5 180915260 4103136 0.02267987786104942 0.1630006148219683 chr6 171115067 3921919 0.022919775965724865 0.18458953401709388 chr7 159138663 3774520 0.023718434784135392 0.255162810644687 chr8 146364022 3447957 0.02355740811768619 0.20335888351932016 chr9 141213431 2838721 0.020102344230981825 0.18362058481376745 chr10 135534747 3279230 0.02419475501732408 0.21487369045976237 chr11 135006516 3015203 0.022333759060933028 0.18975116839614736 chr12 133851895 3034091 0.022667523683545906 0.1635877089612598 chr13 115169878 2090661 0.018152845486212984 0.14594131052971188 chr14 107349540 2038062 0.01898528861884271 0.15049305644206049 chr15 102531392 1953360 0.01905133600448924 0.1500588559113757 chr16 90354753 1993773 0.02206605556212411 0.1683130436386919 chr17 81195210 1854814 0.02284388450993599 0.16919103340663433 chr18 78077248 1769606 0.022664810112159692 0.27909739596006167 chr19 59128983 1443526 0.02441317145603536 0.2839655850703298 chr20 63025520 1464177 0.02323149416299937 0.1657703260497189 chr21 48129895 902552 0.018752419883733384 0.15962813604030016 chr22 51304566 822219 0.01602623439013206 0.13622653165581938 chrMT 16571 2831 0.17084062518858245 0.41814425683192263 chrX 155270560 3841479 0.024740549657320744 0.1828055356201552 chrY 59373566 210215 0.0035405486677354027 0.09898745003948946