BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008695.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 = 761,741 number of mapped reads = 647,156 (84.96%) number of supplementary alignments = 3,051 (0.4%) number of secondary alignments = 0 number of mapped bases = 40,969,016 bp number of sequenced bases = 40,940,457 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,135 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8645 >>>>>>> ACTG content number of A's = 11,123,765 bp (27.17%) number of C's = 7,368,565 bp (18%) number of T's = 12,653,929 bp (30.91%) number of G's = 9,789,763 bp (23.91%) number of N's = 4,435 bp (0.01%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 405,768 number of insertions = 3,947 mapped reads with insertion percentage = 0.6% number of deletions = 17,384 mapped reads with deletion percentage = 2.65% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 0.1676X There is a 1.22% of reference with a coverageData >= 1X There is a 0.07% 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 2839430 0.011391867304515161 0.22869985561840314 chr2 243199373 3700045 0.015214040046065415 0.214245955984384 chr3 198022430 2838690 0.014335194250469505 0.12915634220622174 chr4 191154276 1991672 0.010419186228405375 0.11360580072444851 chr5 180915260 2075691 0.01147327759968949 0.11429785418806407 chr6 171115067 2416271 0.014120737830760397 0.1379168477766559 chr7 159138663 2626189 0.016502520195233763 0.27001802096083005 chr8 146364022 3552375 0.02427082114483025 0.19360104945721993 chr9 141213431 1301422 0.009215993059470384 0.1558389992310712 chr10 135534747 2292441 0.016914046403170693 0.16839277068110578 chr11 135006516 1904510 0.014106800593239514 0.21502903983829189 chr12 133851895 1651310 0.012336844390585579 0.12026033662508426 chr13 115169878 1167818 0.010139960380960029 0.1081578688238532 chr14 107349540 1394352 0.012988895900252576 0.12807906290335414 chr15 102531392 1097370 0.010702770913321844 0.11218962234906552 chr16 90354753 992926 0.01098919500117498 0.11807589555543171 chr17 81195210 1029899 0.012684233466481582 0.13978009413236378 chr18 78077248 709225 0.009083632148510152 0.22747270594888394 chr19 59128983 871409 0.014737425806900822 0.16970798725049266 chr20 63025520 850626 0.013496532833049215 0.12945570016956587 chr21 48129895 528139 0.01097320075184041 0.1162970228360534 chr22 51304566 503639 0.009816650627158604 0.1053012359068605 chrMT 16571 30713 1.8534186228954197 1.845431793778008 chrX 155270560 2475762 0.01594482559990767 0.14228092213119906 chrY 59373566 127092 0.0021405485397323113 0.06111658977578308