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
A3 F2 I1 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	217,968	C→T	21.7%	intergenic (‑60/‑46)	yafU ← / → yafF	predicted inner membrane protein/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	217,968	0	C	T	21.7%	369.8 / 92.1	189	intergenic (‑60/‑46)	yafU/yafF	predicted inner membrane protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (64/84); new base T (19/22); total (83/106)
Fisher's exact test for biased strand distribution p-value = 7.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01

Only 100 of 190 total aligned reads displayed.

GAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATA  >  Exported/217901‑218037

gAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAGGTTCGCCACAGCAATCCGAAACCa                                                                     >  1:3018440/1‑70 (MQ=255)

 aaCTAATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCa                                                                     <  1:1460499/69‑1 (MQ=255)

         ataaATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTg                                                           >  1:1605096/1‑71 (MQ=255)

         ataaATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTg                                                           <  1:1512108/71‑1 (MQ=255)

            aaTTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACg                                                             <  1:4754874/66‑1 (MQ=255)

               tCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGaa                                                      >  1:5215661/1‑70 (MQ=255)

                  tcagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGATAATAAg                                                  <  1:914249/68‑1 (MQ=255)

                   tGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATa                                                    <  1:2511962/68‑1 (MQ=255)

                   cagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGc                                                 >  1:1800812/3‑71 (MQ=255)

                    agTTCTGCTGATTTAACCGCAGAGAAGATCGCCACAGCAATCCGAACCCACTGGCATGTCGAGAATAAGc                                                 >  1:2274820/2‑70 (MQ=255)

                     gTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTg                                               <  1:2634944/71‑1 (MQ=255)

                      ttCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCAc                                                                    <  1:2789026/49‑1 (MQ=255)

                       tCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                 >  1:2127757/1‑67 (MQ=255)

                        ctgctgATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCAc                                                                    >  1:4101966/1‑47 (MQ=25)

                        ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                             <  1:3278884/70‑1 (MQ=255)

                        ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                             <  1:1709404/70‑1 (MQ=255)

                        ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                             <  1:2322516/70‑1 (MQ=255)

                        ctgctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGcac                                            >  1:775220/1‑71 (MQ=255)

                         tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                               <  1:3371385/67‑1 (MQ=255)

                         tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                               <  1:2292927/67‑1 (MQ=255)

                         tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGCCATGTGGAGAATAAGCTg                                               <  1:1386567/67‑1 (MQ=255)

                          gctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGaa                                                      <  1:888866/59‑1 (MQ=255)

                           ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTgg                                                                 >  1:3438182/1‑47 (MQ=255)

                           ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTga                                                                 >  1:5483034/1‑46 (MQ=255)

                           ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTAGCATGTGGAGAATAAGCTGCACTgg                                         >  1:5356633/1‑71 (MQ=255)

                              aTTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAg                                                  >  1:2922580/1‑59 (MQ=255)

                               tttAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTc                                     >  1:3650968/1‑71 (MQ=255)

                                ttAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACg                                                             >  1:1863310/1‑46 (MQ=25)

                                ttAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCt                                    >  1:456631/1‑71 (MQ=255)

                                 tAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                   >  1:2033247/1‑71 (MQ=255)

                                 tAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                 >  1:4052539/1‑57 (MQ=255)

                                  aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                                   <  1:3691445/70‑1 (MQ=255)

                                   aCCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                   <  1:1220340/69‑1 (MQ=255)

                                    ccGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcac                                            <  1:789490/59‑1 (MQ=255)

                                     cGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACg                               <  1:4357549/71‑1 (MQ=255)

                                     cGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGgag                                                        <  1:3727569/46‑1 (MQ=255)

                                      gCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGt                              <  1:320840/71‑1 (MQ=255)

                                       ctgagaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTg                             >  1:1464334/3‑71 (MQ=255)

                                       cAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                             >  1:316088/1‑55 (MQ=255)

                                        agagAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                               <  1:4280936/52‑1 (MQ=255)

                                        agagAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTgg                            <  1:5525763/71‑1 (MQ=255)

                                         gagaAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                           <  1:2267324/71‑1 (MQ=255)

                                         gaaaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                           <  1:1425037/68‑1 (MQ=255)

                                          agaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                           <  1:4600385/70‑1 (MQ=255)

                                           gaAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaa                         >  1:5564911/1‑71 (MQ=255)

                                            aaattCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACg                               <  1:2987081/61‑1 (MQ=255)

                                            aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                   <  1:1060063/60‑1 (MQ=38)

                                            aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                        >  1:2452531/1‑71 (MQ=255)

                                            aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                        >  1:3358243/1‑71 (MQ=255)

                                            aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                 >  1:1007590/1‑46 (MQ=255)

                                             aGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                        <  1:4325223/70‑1 (MQ=255)

                                             aGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg                       <  1:231813/71‑1 (MQ=255)

                                             aGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg                       <  1:5414985/71‑1 (MQ=255)

                                              attCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATa                                                    <  1:2619449/40‑1 (MQ=38)

                                              attCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                       >  1:3880512/2‑70 (MQ=255)

                                               ttCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGca                                             >  1:5407114/1‑47 (MQ=255)

                                                 cGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaat                    >  1:4831018/1‑70 (MQ=255)

                                                  gCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaatg                   >  1:4191845/1‑70 (MQ=39)

                                                  gCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                       <  1:1666448/66‑1 (MQ=255)

                                                   ccACAGCAATCCGAAACCACTGGCACGTGGATAATAAGCTGCACAGGCGTCTGGACGt                              <  1:1691448/58‑1 (MQ=255)

                                                   ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:479102/71‑1 (MQ=255)

                                                   ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:949904/71‑1 (MQ=255)

                                                    cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACg                               >  1:258264/1‑56 (MQ=38)

                                                    cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                     <  1:3630250/66‑1 (MQ=39)

                                                    cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                     <  1:2563555/66‑1 (MQ=39)

                                                     acaGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAga               >  1:1180948/1‑71 (MQ=255)

                                                      caGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTgt                                  <  1:2411341/51‑2 (MQ=255)

                                                      caGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac              <  1:1755055/71‑1 (MQ=255)

                                                      caGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                                   <  1:3084127/50‑1 (MQ=255)

                                                       aGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacg             <  1:2897789/71‑1 (MQ=255)

                                                        gCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgacga            >  1:2762749/1‑71 (MQ=255)

                                                         cgaTCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacgac           >  1:4682176/3‑71 (MQ=255)

                                                         cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                     <  1:93979/61‑1 (MQ=38)

                                                         cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:153989/65‑1 (MQ=39)

                                                         cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:1723496/65‑1 (MQ=39)

                                                         cAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga            <  1:4896869/70‑1 (MQ=255)

                                                           aTCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTgg                            <  1:2915520/52‑1 (MQ=255)

                                                           aTCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg         >  1:2484164/1‑70 (MQ=255)

                                                           aTCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg         >  1:3663167/1‑70 (MQ=255)

                                                            tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                      <  1:4398494/41‑1 (MQ=25)

                                                            tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                      <  1:5121478/41‑1 (MQ=25)

                                                            tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg         >  1:3170285/1‑69 (MQ=39)

                                                            tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac              <  1:3384762/65‑1 (MQ=255)

                                                            tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac              <  1:1304847/65‑1 (MQ=255)

                                                            tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGt                                      <  1:1212738/41‑1 (MQ=255)

                                                            tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGt                                      <  1:629880/41‑1 (MQ=255)

                                                             ccGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 >  1:2045651/1‑61 (MQ=255)

                                                             ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg                       <  1:4846693/55‑1 (MQ=255)

                                                             ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:4957015/61‑1 (MQ=255)

                                                             ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTAc        >  1:3331895/1‑70 (MQ=255)

                                                             ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTAc        >  1:3945071/1‑70 (MQ=255)

                                                              cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:349716/60‑1 (MQ=255)

                                                              cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:2216808/60‑1 (MQ=255)

                                                              cGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa       >  1:3812282/1‑70 (MQ=38)

                                                              cGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCt                                    >  1:1119557/1‑41 (MQ=255)

                                                               gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga            >  1:5029932/1‑64 (MQ=255)

                                                               gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga            >  1:85915/1‑64 (MQ=255)

                                                               gAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                 <  1:1950028/59‑1 (MQ=255)

                                                                aaaCCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACaaaa    >  1:1000416/1‑71 (MQ=255)

                                                                  aCCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCaaaa    >  1:716916/1‑69 (MQ=39)

GAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATA  >  Exported/217901‑218037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A