BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524345.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 = 472,227 number of mapped reads = 435,940 (92.32%) number of supplementary alignments = 2,014 (0.43%) number of secondary alignments = 0 number of mapped bases = 25,547,763 bp number of sequenced bases = 25,540,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,079 duplication rate = 1.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8019 >>>>>>> ACTG content number of A's = 6,474,987 bp (25.35%) number of C's = 4,884,074 bp (19.12%) number of T's = 7,684,451 bp (30.09%) number of G's = 6,494,017 bp (25.43%) number of N's = 3,220 bp (0.01%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 129,195 number of insertions = 1,447 mapped reads with insertion percentage = 0.33% number of deletions = 4,362 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 0.1107X There is a 0.79% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2198880 0.008821963978176006 0.1739866956233972 chr2 243199373 1662106 0.006834335053980588 0.12141075898089315 chr3 198022430 1773168 0.008954379561951643 0.09716702285975928 chr4 191154276 1318892 0.006899620702180892 0.0900863743406362 chr5 180915260 1494883 0.008262890593087614 0.09308165578967752 chr6 171115067 1596977 0.009332766704874679 0.10194156480845763 chr7 159138663 1166066 0.007327358279992587 0.11803223266283022 chr8 146364022 2658701 0.018164990027398947 0.152234811256498 chr9 141213431 1057380 0.007487814668280385 0.09612527382091508 chr10 135534747 1317608 0.009721551330302038 0.11299730049406412 chr11 135006516 1232209 0.009127033542588418 0.10432957532810284 chr12 133851895 997992 0.007455942256177995 0.08890374347504829 chr13 115169878 629899 0.005469303353781446 0.07535027228569643 chr14 107349540 528854 0.004926467314158961 0.07310172603152806 chr15 102531392 782457 0.007631389613826758 0.08910232113994675 chr16 90354753 817384 0.009046386303551734 0.0995959673197304 chr17 81195210 814620 0.010032857849619454 0.10617514035258113 chr18 78077248 606367 0.007766244527471051 0.13615268838232192 chr19 59128983 457899 0.007744070281066732 0.11432619938517372 chr20 63025520 592525 0.009401350437092785 0.10036343058809047 chr21 48129895 364986 0.007583353339956383 0.09310240177818979 chr22 51304566 198690 0.0038727547173871427 0.06368195147061505 chrMT 16571 2515 0.15177116649568523 0.4530921928348061 chrX 155270560 1198209 0.007716910404651081 0.0929680490985722 chrY 59373566 78496 0.00132206982481059 0.051034275607677315