BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054569.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 15,742,501 number of mapped reads = 11,787,695 (74.88%) number of supplementary alignments = 363 (0%) number of secondary alignments = 0 number of mapped bases = 554,096,066 bp number of sequenced bases = 553,979,828 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,060,271 duplication rate = 22.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4431 >>>>>>> ACTG content number of A's = 167,405,593 bp (30.22%) number of C's = 110,608,492 bp (19.97%) number of T's = 160,879,599 bp (29.04%) number of G's = 114,969,231 bp (20.75%) number of N's = 116,913 bp (0.02%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 3,003,808 number of insertions = 24,747 mapped reads with insertion percentage = 0.21% number of deletions = 77,964 mapped reads with deletion percentage = 0.66% homopolymer indels = 46.67% >>>>>>> Coverage mean coverageData = 0.179X std coverageData = 1.611X There is a 5.32% of reference with a coverageData >= 1X There is a 2.52% of reference with a coverageData >= 2X There is a 1.65% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.76% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 46982138 0.18849356447541207 1.7192068615972544 chr2 243199373 56999432 0.23437326871726763 1.9312642556582018 chr3 198022430 35932364 0.18145603000629776 1.5394615702671988 chr4 191154276 26465360 0.1384502641206938 1.3291115952024788 chr5 180915260 28011657 0.15483302514116276 1.398170471463002 chr6 171115067 34089506 0.19921977998582674 1.7511197385906647 chr7 159138663 29045762 0.1825185750115294 1.6704354421486136 chr8 146364022 29727866 0.20310910832991458 1.7750619565357308 chr9 141213431 29570960 0.20940614352752324 1.7377950004856006 chr10 135534747 19126683 0.14112014389933528 1.3799449216967903 chr11 135006516 26690998 0.19770155390129465 1.709673121935 chr12 133851895 29592561 0.22108436343019275 1.7643163937545705 chr13 115169878 13542103 0.11758372271610812 1.2054115182079357 chr14 107349540 10740828 0.10005471844592906 1.2274134417940397 chr15 102531392 16723737 0.1631084556035287 1.4868352572330947 chr16 90354753 13562489 0.15010266255722043 1.388953135845001 chr17 81195210 15465423 0.19047211036217532 1.6656120851376406 chr18 78077248 17359879 0.22234235253783535 1.8637082890079066 chr19 59128983 11559931 0.19550363313368674 1.7319789309061195 chr20 63025520 11993105 0.19028966361562744 1.5967799678544021 chr21 48129895 5341451 0.11097990136899322 1.2340605042731654 chr22 51304566 7681952 0.14973232596880365 1.39252618429947 chrMT 16571 26815 1.6181884014241747 4.691300299163249 chrX 155270560 36572550 0.23554078764190714 1.8797111808852616 chrY 59373566 1290516 0.02173553126318874 0.45866039558455995