Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F3 I0 R2	260	44.3	3360226	90.5%	3041004	64.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,904,315	A→G	28.0%	intergenic (‑241/‑52)	ygcF ← / → ygcG	conserved hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,904,315	0	A	G	28.0%	75.1 / 33.9	50	intergenic (‑241/‑52)	ygcF/ygcG	conserved hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (32/4); new base G (10/4); total (42/8)
Fisher's exact test for biased strand distribution p-value = 1.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTCACCAAAATTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACT  >  W3110S.gb/2904256‑2904383

cATTCACCAAAATTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATgcc                                                           <  1:1770624/71‑1 (MQ=255)

cATTCACCAAAATTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATgcc                                                           <  1:1128784/71‑1 (MQ=255)

         aaaTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTAcc                                                                 <  1:1015971/56‑1 (MQ=255)

         aaaTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTAcc                                                                 <  1:1699960/56‑1 (MQ=255)

         aaaTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTAcc                                                                 <  1:2334719/56‑1 (MQ=255)

         aaaTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTAcc                                                                 <  1:2799379/56‑1 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:2031978/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:860137/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:1761328/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:2365722/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:550332/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:2837782/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:2842368/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:495652/1‑56 (MQ=255)

           aTTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:1071246/1‑56 (MQ=255)

           aTTATATTTATTCTTTCTGTATTAGTTTTTAATGATAACGAATATAAAGTTACCGa                                                               >  1:2976970/1‑56 (MQ=255)

                       ttttCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGAt                                    >  1:2102342/1‑71 (MQ=255)

                       ttttCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGAt                                    >  1:1885929/1‑71 (MQ=255)

                       ttttCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGAt                                    >  1:2606861/1‑71 (MQ=255)

                       ttttCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGAt                                    >  1:1175088/1‑71 (MQ=255)

                       ttttCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGAt                                    >  1:1524151/1‑71 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:383545/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:3153595/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:2166947/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:1292417/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:2356704/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:279818/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:1807880/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAattta                                               >  1:895328/1‑45 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTta                     >  1:2683138/1‑71 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTta                     >  1:3355133/1‑71 (MQ=255)

                                      tttAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTta                     >  1:3344483/1‑71 (MQ=255)

                                        tAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTtat                    <  1:2430433/70‑1 (MQ=255)

                                        tAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTtat                    <  1:342048/70‑1 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCt            >  1:1647641/1‑67 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAttt        >  1:1339131/1‑71 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAttt        >  1:1672208/1‑71 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAttt        >  1:624690/1‑71 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAttt        >  1:1790019/1‑71 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAtt         >  1:1387982/1‑70 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAtt         >  1:1191859/1‑70 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAtt         >  1:2151626/1‑70 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAtt         >  1:1788579/1‑70 (MQ=255)

                                                   aaTATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTAtt         >  1:3325146/1‑70 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:45362/1‑71 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:101842/1‑71 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:3184239/1‑71 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:2879831/1‑71 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:2578985/1‑71 (MQ=255)

                                                       taAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATa    >  1:1901756/1‑71 (MQ=255)

                                                         aaaTTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACt  <  1:3229554/71‑1 (MQ=255)

                                                         aaaTTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACt  <  1:3117214/71‑1 (MQ=255)

                                                         aaaTTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACt  <  1:1764738/71‑1 (MQ=255)

                                                         aaaTTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACt  <  1:9551/71‑1 (MQ=255)

                                                          aaTTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACt  <  1:150600/70‑1 (MQ=255)

CATTCACCAAAATTATATTTATTTTTTCTGTATTAGTTTTTAATGATAACGAATATAAAATTACCGATGCCGCCGTCAATTTATTTATCCAGATTTAATGAGAAATTTATAATGCGCTATTTCATACT  >  W3110S.gb/2904256‑2904383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A