BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716580.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 = 1,207,614 number of mapped reads = 1,077,718 (89.24%) number of supplementary alignments = 5,909 (0.49%) number of secondary alignments = 0 number of mapped bases = 62,758,875 bp number of sequenced bases = 62,740,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,776 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.496 >>>>>>> ACTG content number of A's = 16,110,565 bp (25.68%) number of C's = 12,005,221 bp (19.13%) number of T's = 19,866,192 bp (31.66%) number of G's = 14,757,210 bp (23.52%) number of N's = 839 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 309,849 number of insertions = 4,898 mapped reads with insertion percentage = 0.45% number of deletions = 11,826 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2207X There is a 1.86% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 4992340 0.02002939844230117 0.29498576382546393 chr2 243199373 5852437 0.02406435891592533 0.26577445101569597 chr3 198022430 4602979 0.023244735457493376 0.164922822335641 chr4 191154276 3344050 0.017493984806282857 0.15526902996733516 chr5 180915260 3237660 0.017896002802638096 0.14209165419575873 chr6 171115067 3328670 0.01945281650738564 0.15559499101030025 chr7 159138663 4060219 0.02551371818424791 0.49131147545515147 chr8 146364022 4985676 0.03406353509471064 0.2407439131091513 chr9 141213431 2502496 0.01772137382597835 0.1549441515561407 chr10 135534747 2919985 0.021544180106080103 0.2564866572118049 chr11 135006516 2032337 0.015053621560014184 0.14975348208358452 chr12 133851895 3257640 0.024337645724029532 0.17315922035319806 chr13 115169878 1951541 0.016944890746519677 0.1376757546799829 chr14 107349540 1929650 0.017975391417606446 0.14321002735437163 chr15 102531392 1428522 0.013932532974876611 0.1261337591913095 chr16 90354753 1865952 0.020651398382993753 0.15713221313893522 chr17 81195210 2566428 0.03160812072534821 0.19553514279443424 chr18 78077248 1442832 0.018479544770840284 0.22774173787012855 chr19 59128983 1231519 0.020827670924088108 0.2621362973940211 chr20 63025520 1346523 0.021364726542518014 0.15979831128674488 chr21 48129895 485979 0.010097237901724074 0.11714146825217267 chr22 51304566 980556 0.019112450926882414 0.14639686520503115 chrMT 16571 143755 8.675095045561523 5.532550331701162 chrX 155270560 2121276 0.013661804272490549 0.13578005504263457 chrY 59373566 147853 0.002490215932120365 0.0829607167641661