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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,879,768	A→G	29.5%	R86R (CGT→CGC)	ytfE ←	predicted regulator of cell morphogenesis and cell wall metabolism

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,879,768	0	A	G	29.5%	75.3 / 36.4	81	R86R (CGT→CGC)	ytfE	predicted regulator of cell morphogenesis and cell wall metabolism
Reads supporting (aligned to +/- strand): ref base A (20/37); new base G (12/12); total (32/49)
Fisher's exact test for biased strand distribution p-value = 2.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.47e-01

TTTGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGT  >  minE/2879702‑2879829

tttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACg                                                             <  1:360231/69‑1 (MQ=255)

tttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACg                                                             <  1:3095735/69‑1 (MQ=255)

tttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACg                                                             <  1:2559664/69‑1 (MQ=255)

 ttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGa                                                            <  1:854344/69‑1 (MQ=255)

 ttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGa                                                            <  1:2909108/69‑1 (MQ=255)

 ttGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGa                                                            <  1:159181/69‑1 (MQ=255)

          tGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAg                                                   >  1:1157693/1‑69 (MQ=255)

          tGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAg                                                   <  1:3129052/69‑1 (MQ=255)

          tGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAg                                                   >  1:2261680/1‑69 (MQ=255)

                cgcTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACg                                             <  1:3417588/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:2563164/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:703820/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:2922079/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:250593/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:2456059/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:1706051/69‑1 (MQ=255)

                    cGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatga                                         <  1:1340547/69‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGGAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:3035146/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:74656/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:746077/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:1567975/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:2239784/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:61440/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:1238211/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:432664/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:523905/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:1961428/51‑1 (MQ=255)

                          tAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGt                                                     <  1:2008808/51‑1 (MQ=255)

                            gTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTc                                  <  1:1607015/68‑1 (MQ=255)

                            gTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTc                                  <  1:181041/68‑1 (MQ=255)

                            gTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTc                                  <  1:1204648/68‑1 (MQ=255)

                            gTCGCATGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTc                                  <  1:1725413/68‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:575671/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1281608/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:3159589/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1299579/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:616340/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1329618/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:2673742/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1497352/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:2549177/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1438679/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1645400/69‑1 (MQ=255)

                               gCTTGCAGGATCAGCTCCGGCAGCTGCTCGCGATGGCGATCGTGATAGCGCACAATAATGTGGTCgatg                              <  1:1617320/69‑1 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:2189597/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:3146866/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:1324964/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:3035726/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:2950904/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:2886438/1‑69 (MQ=255)

                               gCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatg                              >  1:875324/1‑69 (MQ=255)

                                 ttGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCgatgat                            <  1:3149656/69‑1 (MQ=255)

                                  tGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGt                                                        >  1:1411878/1‑40 (MQ=255)

                                  tGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGt                                                        >  1:2770552/1‑40 (MQ=255)

                                         tCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTTGTAg                                                   >  1:2883071/1‑38 (MQ=255)

                                         tCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGcc                     >  1:1527682/1‑68 (MQ=255)

                                         tCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCa                    >  1:826492/1‑69 (MQ=255)

                                         tCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCa                    >  1:1199181/1‑69 (MQ=255)

                                         tCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCAATGATTTCTGCCa                    >  1:305662/1‑69 (MQ=255)

                                           aGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:631589/45‑1 (MQ=255)

                                           aGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:1903781/45‑1 (MQ=255)

                                           aGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:2089307/45‑1 (MQ=255)

                                           aGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:1043562/45‑1 (MQ=255)

                                           aGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:3092552/45‑1 (MQ=255)

                                            gCTCCTGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACgatg                                          <  1:584639/44‑1 (MQ=255)

                                                       tGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTAc        >  1:444233/1‑67 (MQ=255)

                                                       tGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTAc        >  1:2548437/1‑67 (MQ=255)

                                                       tGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTAc        >  1:1721792/1‑67 (MQ=255)

                                                       tGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTAc        >  1:3073388/1‑67 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:979180/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:3342438/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:1410127/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:2678012/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:291917/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:303441/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:733574/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:1782076/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:1786053/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:2381560/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:3308865/1‑69 (MQ=255)

                                                           cgcgATGGCGATCGTGATAGCGCACAATAATGTGGTCGATGATTTCCGCCAGCGGGGCGCTACGCCAGt  >  1:2108688/1‑69 (MQ=255)

TTTGTCGGCGTGAACGCGCTCGACTTTAGTCGCTTGCAGAATCAGCTCCGGCAGTTGCTCGCGGTGACGATCGTGGTAGCGCACGATGATATGGTCGATGATTTCTGCCAGCGGGGCGCTACGCCAGT  >  minE/2879702‑2879829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A