BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234121.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 = 719,092 number of mapped reads = 459,301 (63.87%) number of supplementary alignments = 2,286 (0.32%) number of secondary alignments = 0 number of mapped bases = 30,314,731 bp number of sequenced bases = 30,299,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,104 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7642 >>>>>>> ACTG content number of A's = 8,659,706 bp (28.58%) number of C's = 5,179,047 bp (17.09%) number of T's = 9,848,492 bp (32.5%) number of G's = 6,607,923 bp (21.81%) number of N's = 4,358 bp (0.01%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 268,117 number of insertions = 2,577 mapped reads with insertion percentage = 0.56% number of deletions = 8,647 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 0.1297X There is a 0.9% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 5537066 0.022214853378439526 0.22215420425682655 chr2 243199373 1806380 0.00742756849130528 0.11190604351052742 chr3 198022430 4872282 0.02460469755875635 0.16800499730806298 chr4 191154276 328938 0.0017207985449407368 0.047322628958820785 chr5 180915260 1847714 0.01021314619894419 0.10703932661706592 chr6 171115067 638442 0.003731068287516727 0.07317824093057558 chr7 159138663 728731 0.004579220324353234 0.0823886086031053 chr8 146364022 1953109 0.013344187822332458 0.25294663494879116 chr9 141213431 1670471 0.011829405943688176 0.12215718231571375 chr10 135534747 258805 0.0019095103339072158 0.07405373321217551 chr11 135006516 2005707 0.014856371821342312 0.14398968018617542 chr12 133851895 523593 0.0039117339354814516 0.06663677978405588 chr13 115169878 1166587 0.010129271822272834 0.10696046096040072 chr14 107349540 1612598 0.015021936749798835 0.13124979929388345 chr15 102531392 249081 0.002429314526423283 0.05295487609411252 chr16 90354753 881621 0.009757328427426501 0.1084815209084307 chr17 81195210 232453 0.0028628905572139047 0.06437717355642597 chr18 78077248 509061 0.006519965970112061 0.14144646554039736 chr19 59128983 717609 0.012136332532558525 0.13996064203206612 chr20 63025520 477435 0.007575264749898137 0.09235845952475882 chr21 48129895 735154 0.015274373650721656 0.13266329019998654 chr22 51304566 342831 0.006682270735902922 0.09638801426572445 chrMT 16571 3032 0.18297024923058355 0.48909205316496435 chrX 155270560 1143510 0.007364628555471172 0.09401243838187563 chrY 59373566 72521 0.0012214358153929982 0.04260707431648867