BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524997.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 = 3,491,479 number of mapped reads = 3,138,030 (89.88%) number of supplementary alignments = 9,428 (0.27%) number of secondary alignments = 0 number of mapped bases = 179,340,155 bp number of sequenced bases = 179,281,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,713 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7321 >>>>>>> ACTG content number of A's = 46,463,168 bp (25.92%) number of C's = 31,637,530 bp (17.65%) number of T's = 56,408,669 bp (31.46%) number of G's = 44,770,460 bp (24.97%) number of N's = 1,705 bp (0%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 895,295 number of insertions = 14,397 mapped reads with insertion percentage = 0.46% number of deletions = 35,099 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0579X std coverageData = 0.4894X There is a 4.96% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19698730 0.07903181914238841 1.0389809770406153 chr2 243199373 16899341 0.06948760102272139 0.560361544946221 chr3 198022430 10093989 0.050973967948984365 0.2652379307054001 chr4 191154276 11790572 0.0616809220631821 0.3185363566252578 chr5 180915260 8000916 0.0442246607610657 0.24986232843341183 chr6 171115067 10762593 0.06289681667833494 0.4792814965001953 chr7 159138663 10895497 0.06846543005077277 0.6748188250599578 chr8 146364022 10865856 0.07423857209936469 0.4404556067832527 chr9 141213431 4655016 0.03296439982397992 0.35280335213317715 chr10 135534747 9343075 0.06893490567404091 0.47133908462736657 chr11 135006516 7679569 0.05688295074587363 0.4109109503068691 chr12 133851895 9968398 0.07447334234603104 0.3186514804554824 chr13 115169878 3607414 0.03132254772380674 0.2101802573674796 chr14 107349540 4192076 0.039050712280648804 0.23549759099772943 chr15 102531392 5073552 0.04948291348663247 0.30208182142588286 chr16 90354753 5849411 0.0647382766903253 0.3176194027143295 chr17 81195210 4738322 0.05835716170941611 0.427293991499975 chr18 78077248 3686294 0.04721342125173264 0.6025455940166999 chr19 59128983 4554894 0.0770331869229004 0.6107527828791498 chr20 63025520 3432572 0.05446320791958559 0.27352310650531786 chr21 48129895 2694904 0.055992309976990395 0.28927295234604244 chr22 51304566 2529572 0.0493050072775199 0.2518951930197224 chrMT 16571 41702 2.516565083579748 2.1504900274961933 chrX 155270560 7787722 0.05015581833413881 0.3350922561715857 chrY 59373566 498168 0.008390400536157791 0.18178522596843763