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 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,404,628	A→C	12.4%	intergenic (+315/‑663)	yhdH → / → accB	predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,404,628	0	A	C	12.4%	166.4 / 25.6	81	intergenic (+315/‑663)	yhdH/accB	predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit
Reads supporting (aligned to +/- strand): ref base A (42/29); new base C (5/5); total (47/34)
Fisher's exact test for biased strand distribution p-value = 7.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CGCTACGCTTAGCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCA  >  W3110S.gb/3404560‑3404695

cgctacgctTAGCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAAtt                                                                   <  1:1981176/71‑1 (MQ=255)

     cgctTAGCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAACTTAAt                                                                <  1:442675/69‑1 (MQ=255)

          aGCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCg                                                          <  1:740058/70‑1 (MQ=255)

           gCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGaa                                                        >  1:4498584/1‑71 (MQ=255)

           gCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGa                                                         <  1:2050685/70‑1 (MQ=255)

              ccTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACaaa                                                                     <  1:994374/55‑1 (MQ=255)

               cttacttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTa                                                    <  1:3901037/71‑1 (MQ=255)

                ttacttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTa                                                    >  1:890535/1‑70 (MQ=255)

                  acttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTAtt                                                  >  1:1747581/1‑70 (MQ=255)

                   cttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAttt                                                 >  1:637880/1‑70 (MQ=255)

                   cttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAttt                                                 <  1:1783620/70‑1 (MQ=255)

                    ttaTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAttt                                                 <  1:283200/69‑1 (MQ=255)

                      aTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:29058/1‑69 (MQ=255)

                      aTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:2583326/1‑69 (MQ=255)

                      aTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTa                                                >  1:4353038/1‑68 (MQ=255)

                      aTTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATg                                             >  1:2698858/1‑71 (MQ=255)

                        ttCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:4541314/1‑67 (MQ=255)

                         tCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAAc                                                       >  1:384041/1‑58 (MQ=255)

                         tCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCt                                           <  1:2515701/70‑1 (MQ=255)

                          cTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTg                                          <  1:3579894/70‑1 (MQ=255)

                              tACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAg                                        <  1:4022512/68‑1 (MQ=255)

                               aCCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAtt                                    >  1:2084803/1‑71 (MQ=255)

                               aCCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAtt                                    >  1:2898155/1‑71 (MQ=255)

                               aCCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAtt                                    >  1:2574290/1‑71 (MQ=255)

                                ccATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATg                                             >  1:1821901/1‑61 (MQ=255)

                                  aTGGGGTGAATAATCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCATTGt                                  >  1:2684201/1‑70 (MQ=255)

                                  aTGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGaa                                                        >  1:1623766/1‑48 (MQ=255)

                                  aTGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:2082787/1‑57 (MQ=255)

                                  aTGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGt                                  >  1:3958916/1‑70 (MQ=255)

                                   tGGGGTGAATAATCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCa                                <  1:3690309/71‑1 (MQ=255)

                                   tGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               <  1:4583603/56‑1 (MQ=255)

                                   tGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               <  1:4347821/56‑1 (MQ=255)

                                    ggggTGAATAATCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCa                                <  1:1026568/70‑1 (MQ=255)

                                    ggggTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:4009007/1‑55 (MQ=255)

                                     gggTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAAt                              >  1:2397520/1‑71 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAtt                                                  >  1:713448/1‑46 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAt                                                   >  1:2709476/1‑45 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATg                                             <  1:4011734/51‑1 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATg                                             <  1:1270412/51‑1 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAt                                     >  1:3911005/1‑59 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAt                                     >  1:3429704/1‑59 (MQ=255)

                                          aataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGt                          >  1:2749694/1‑70 (MQ=255)

                                           ataatCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTAttt                                                 <  1:2806982/46‑1 (MQ=255)

                                            taatCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTaa                       >  1:1728382/1‑71 (MQ=255)

                                              atCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAAt                      <  1:2556144/70‑1 (MQ=255)

                                              atCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAAt                      <  1:97385/70‑1 (MQ=255)

                                               tCTGATTTTGTTTGACTACAACTTAATCACTCGAACCTCTTTAAt                                              <  1:10879/45‑1 (MQ=38)

                                               tCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGc                                            >  1:3662417/1‑47 (MQ=255)

                                               tCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGc                                            >  1:1351920/1‑47 (MQ=255)

                                               tCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAAttt                    >  1:1346102/1‑71 (MQ=255)

                                               tCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAAtt                     >  1:1842920/1‑70 (MQ=255)

                                                 tGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTaa                                               >  1:2700166/1‑42 (MQ=255)

                                                 tGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTc                                 <  1:745864/56‑1 (MQ=255)

                                                  gATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGc                 >  1:4160931/1‑71 (MQ=255)

                                                  gATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGc                 >  1:832460/1‑71 (MQ=255)

                                                   aTTTTGTTTGACTACAAATTAATCACTCGAACCTa                                                    >  1:3211588/1‑35 (MQ=255)

                                                   aTTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAt                                     >  1:3206063/1‑50 (MQ=255)

                                                   aTTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCg                >  1:3155275/1‑71 (MQ=255)

                                                   aTTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCg                >  1:1981101/1‑71 (MQ=255)

                                                   aTTTTGTTTGACTACAAATTAATCACTAGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAAtttt                   <  1:1426842/68‑1 (MQ=255)

                                                     tttgtttgACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCa                                      >  1:1561161/1‑47 (MQ=255)

                                                     tttgtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTg              >  1:3647373/1‑71 (MQ=255)

                                                      ttgtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCa                                      >  1:2213103/1‑46 (MQ=255)

                                                      ttgtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCa                                      >  1:1945159/1‑46 (MQ=255)

                                                      ttgtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTg              <  1:2402430/70‑1 (MQ=255)

                                                       tgtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAg                                        <  1:2937760/43‑1 (MQ=255)

                                                        gtttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCtt           >  1:910672/1‑71 (MQ=255)

                                                         tttgACTACAAATTAATCACTCGAACCTTTTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCttt          <  1:4537285/71‑1 (MQ=255)

                                                         tttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTg                                   <  1:4144613/46‑1 (MQ=255)

                                                          ttgACTACAAATTAATCACTCGAACCTATTTAATGCTGAGc                                       <  1:1242212/41‑1 (MQ=255)

                                                            gACTACAACTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAg        >  1:2118735/1‑70 (MQ=255)

                                                            gACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCAt                                     >  1:2082131/1‑41 (MQ=255)

                                                            gACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAg        <  1:4189186/70‑1 (MQ=255)

                                                            gACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAg        <  1:802118/70‑1 (MQ=255)

                                                            gACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAg        <  1:3757489/70‑1 (MQ=255)

                                                             aCTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCa      <  1:3083564/71‑1 (MQ=255)

                                                             aCTACAAATTAATCACTCGAACCTATTTAATGC‑‑AGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCAtt    <  1:2574349/71‑1 (MQ=255)

                                                               tACAAATTAATCACTCGAACCTATTTAATGCTGAg                                        <  1:2606961/35‑1 (MQ=255)

                                                                aCAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCt            >  1:4319350/1‑62 (MQ=255)

                                                                 cAAATTAATCACTCGAACCTATTTAATGCTGAGCa                                      >  1:3791610/1‑35 (MQ=255)

                                                                 cAAATTAATCACTCGAACCTATTTAATGCTGAGCa                                      >  1:3677376/1‑35 (MQ=255)

                                                                 cAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCAtt    <  1:4629217/69‑1 (MQ=255)

                                                                  aaaTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTa         <  1:1642660/63‑1 (MQ=255)

                                                                  aaaTTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTca  >  1:1913043/1‑70 (MQ=255)

CGCTACGCTTAGCCCCTTACTTATTTCTGGTACCATGGGGTGAATAATCTGATTTTGTTTGACTACAAATTAATCACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCA  >  W3110S.gb/3404560‑3404695

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