BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716262.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 = 515,225 number of mapped reads = 422,499 (82%) number of supplementary alignments = 2,110 (0.41%) number of secondary alignments = 0 number of mapped bases = 24,315,762 bp number of sequenced bases = 24,309,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,786 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6656 >>>>>>> ACTG content number of A's = 6,165,490 bp (25.36%) number of C's = 4,725,722 bp (19.44%) number of T's = 7,598,741 bp (31.26%) number of G's = 5,818,974 bp (23.94%) number of N's = 360 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 118,853 number of insertions = 1,484 mapped reads with insertion percentage = 0.35% number of deletions = 4,240 mapped reads with deletion percentage = 1% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1031X There is a 0.75% of reference with a coverageData >= 1X There is a 0.03% 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 1986309 0.007969123575423308 0.14664245432760867 chr2 243199373 2039010 0.008384108786333097 0.11961623072175356 chr3 198022430 1635185 0.008257574659597906 0.09408014828106064 chr4 191154276 1552266 0.008120487976946957 0.0945581781219554 chr5 180915260 1488807 0.008229305808697398 0.0936374390505615 chr6 171115067 1420238 0.008299900323797904 0.09883434048586959 chr7 159138663 1317945 0.008281739805744126 0.11196750673987667 chr8 146364022 1230358 0.008406150522428251 0.102728192047834 chr9 141213431 1004701 0.007114769415948827 0.09292523000009095 chr10 135534747 1134220 0.008368481331211692 0.10170525400403845 chr11 135006516 1097660 0.00813042238642763 0.09933151604971265 chr12 133851895 1056241 0.00789111726808201 0.09192951041256107 chr13 115169878 758025 0.006581799105491802 0.0835904731176324 chr14 107349540 732358 0.006822181073155973 0.08750969772769349 chr15 102531392 706784 0.006893342479930439 0.08651279691067275 chr16 90354753 727134 0.00804754565595459 0.0936416247251398 chr17 81195210 679176 0.008364729889854339 0.09546330541871416 chr18 78077248 633473 0.008113413526050509 0.11893158277615179 chr19 59128983 519826 0.008791390848038092 0.1186391853939301 chr20 63025520 525071 0.008331085566608575 0.09470605117516226 chr21 48129895 311191 0.006465648844652581 0.08440599234377588 chr22 51304566 298954 0.005827044711770878 0.07889409327042653 chrMT 16571 1391 0.08394182608170901 0.2956279206613007 chrX 155270560 1387316 0.00893482962900372 0.09945019646326622 chrY 59373566 72123 0.0012147324956025044 0.04138628706361272