BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004123.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,179,821 number of mapped reads = 2,457,075 (77.27%) number of supplementary alignments = 14,216 (0.45%) number of secondary alignments = 0 number of mapped bases = 159,081,465 bp number of sequenced bases = 158,999,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,858 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5556 >>>>>>> ACTG content number of A's = 43,342,501 bp (27.26%) number of C's = 27,732,304 bp (17.44%) number of T's = 52,153,978 bp (32.8%) number of G's = 35,754,561 bp (22.49%) number of N's = 16,339 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,655,463 number of insertions = 14,806 mapped reads with insertion percentage = 0.6% number of deletions = 50,137 mapped reads with deletion percentage = 2.02% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.0514X std coverageData = 0.4686X There is a 4.3% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13769944 0.05524537489517428 0.7587658596201724 chr2 243199373 14073375 0.05786764507818036 0.6142453407922913 chr3 198022430 12791192 0.06459466233193886 0.2953504596303674 chr4 191154276 8989537 0.047027653203007606 0.26384837650580906 chr5 180915260 7897880 0.04365513445355577 0.2440362806121854 chr6 171115067 10283844 0.06009899759440821 0.3319009187117189 chr7 159138663 11604294 0.0729193885460757 0.7609754561543628 chr8 146364022 10206059 0.06973065416308388 0.7823410744033127 chr9 141213431 5139506 0.036395305769463246 0.4071355480810507 chr10 135534747 7709048 0.05687875744512955 0.43711728872622196 chr11 135006516 5708007 0.042279492643155094 0.31408349865211654 chr12 133851895 6924831 0.05173502399797926 0.2707723523842613 chr13 115169878 4834043 0.04197315377897683 0.23718457733218315 chr14 107349540 4046778 0.037697208576767074 0.2727521546484412 chr15 102531392 4047274 0.039473510707823026 0.23424877852300596 chr16 90354753 3769420 0.04171800458576872 0.2753770976121022 chr17 81195210 3884485 0.04784130738746781 0.270669088784672 chr18 78077248 4508091 0.05773885626706515 0.825740610908072 chr19 59128983 2852822 0.048247438992820156 0.5246740241320619 chr20 63025520 3744614 0.059414249973661466 0.30393108115518686 chr21 48129895 2226400 0.046258152027965155 0.2688342775542871 chr22 51304566 1793396 0.03495587507747361 0.21256409316359245 chrMT 16571 57561 3.47359845513246 3.238515444892514 chrX 155270560 7841308 0.05050093205048014 0.3049570932299819 chrY 59373566 377756 0.006362359976828745 0.12971748138383066