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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,082,060	A→G	pseudogene (601/726 nt)	efeU →	ferrous iron permease (pseudogene)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,082,060	0	A	G	100.0%	177.1 / NA	49	pseudogene (601/726 nt)	efeU	ferrous iron permease (pseudogene)
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (26/23); total (26/23)

TCGCCGCAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGATTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAATAC  >  NC_000913/1081926‑1082192

tcgCCGCAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGtttt                                                                                                                                   <  1:296994/139‑1 (MQ=255)

              gCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAg                                                                                                                     >  2:1260664/1‑139 (MQ=255)

              gCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAg                                                                                                                     >  2:454349/1‑139 (MQ=255)

                       gCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCg                                                                                                            <  2:795230/139‑1 (MQ=255)

                             cgcgCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCg                                                                                                      <  1:454349/139‑1 (MQ=255)

                              gcgcATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGTCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGa                                                                                                     <  1:805436/139‑1 (MQ=255)

                                           aGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTgg                                                                                        <  2:1142830/139‑1 (MQ=255)

                                            gCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                       >  2:255671/1‑139 (MQ=255)

                                              cGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGttt                                                                                     >  1:460406/1‑139 (MQ=255)

                                              cGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGttt                                                                                     >  2:635122/1‑139 (MQ=255)

                                              cGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGttt                                                                                     >  2:1164514/1‑139 (MQ=255)

                                                       gAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                       >  2:154652/1‑128 (MQ=255)

                                                       gAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGt                                                                                       <  1:154652/128‑1 (MQ=255)

                                                              tttCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCgg                                                                    <  2:43478/139‑1 (MQ=255)

                                                               ttCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                                >  2:747040/1‑79 (MQ=255)

                                                               ttCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                                <  1:747040/79‑1 (MQ=255)

                                                                     aaaTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCtggt                                                             <  1:1164514/139‑1 (MQ=255)

                                                                       aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                                >  1:241362/1‑71 (MQ=255)

                                                                       aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTgg                                                                                                                                <  2:241362/71‑1 (MQ=255)

                                                                       aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCg                                                                                                >  1:831269/1‑103 (MQ=255)

                                                                       aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCg                                                                                                <  2:831269/103‑1 (MQ=255)

                                                                       aTCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTATTTTATCTCATCCCGGCGCtggcg                                                            >  1:638893/1‑137 (MQ=255)

                                                                          gCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCAt                                                        <  2:978095/139‑1 (MQ=255)

                                                                                        tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGt                                                                                                  >  1:277015/1‑84 (MQ=255)

                                                                                        tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGt                                                                                                  <  2:277015/84‑1 (MQ=255)

                                                                                        tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                            <  1:544110/90‑1 (MQ=255)

                                                                                        tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGt                                                                                            >  2:544110/1‑90 (MQ=255)

                                                                                        tGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGccacca                                          >  1:551744/1‑139 (MQ=255)

                                                                                         gCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              >  1:850252/1‑71 (MQ=255)

                                                                                         gCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              <  2:850252/71‑1 (MQ=255)

                                                                                          cGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCAcg                                        >  2:400509/1‑139 (MQ=255)

                                                                                            gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              <  2:1004936/68‑1 (MQ=255)

                                                                                            gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              >  1:1004936/1‑68 (MQ=255)

                                                                                            gTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTCGCTCTGCCACCAcgcg                                      >  1:892374/1‑139 (MQ=255)

                                                                                             tGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACgcgc                                     <  1:1260664/139‑1 (MQ=255)

                                                                                                 ctcAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAggg                                 >  2:686623/1‑139 (MQ=255)

                                                                                                  tcAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAgggg                                >  2:406942/1‑139 (MQ=255)

                                                                                                         actcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCg                                                                                             >  2:622141/1‑72 (MQ=255)

                                                                                                         actcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCg                                                                                             <  1:622141/72‑1 (MQ=255)

                                                                                                         actcGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCCTTTGCTCTGCCACCACGCGCAGGGGCGACAGc                         >  2:228221/1‑139 (MQ=255)

                                                                                                            cGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATc                                                                        >  1:877988/1‑89 (MQ=255)

                                                                                                            cGCTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGCTTTA‑TTTATCTCATc                                                                        <  2:877988/89‑1 (MQ=255)

                                                                                                              cTGTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGtctc                    >  1:442600/1‑139 (MQ=255)

                                                                                                                gTTTGGCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGc                  >  2:192945/1‑139 (MQ=255)

                                                                                                                     gCACGCTGATGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCcgc             <  1:255671/139‑1 (MQ=255)

                                                                                                                             aTGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              <  1:367973/35‑1 (MQ=255)

                                                                                                                             aTGGAAGGGGTTTTTGGCTATCAGGAAGCGCCGAg                                                                                                              >  2:367973/1‑35 (MQ=37)

                                                                                                                               ggAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAATa   <  2:736214/139‑1 (MQ=255)

                                                                                                                                gAAGGGGTTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAATac  <  2:892374/139‑1 (MQ=255)

TCGCCGCAGGGCTGGCAGCTGGTGCCATTCGCGCATTTCATGAAGCCGGATTGTGGAACCACTTTCAGGAAATCGCCTTCGATATGAGTGCGGTGCTCTCAACTCACTCGCTGTTTGGCACGCTGATGGAAGGGATTTTTGGCTATCAGGAAGCGCCGAGCGTCAGCGAAGTCGCCGTCTGGTTTA‑TTTATCTCATCCCGGCGCTGGTGGCATTTGCTCTGCCACCACGCGCAGGGGCGACAGCGTCTCGCTCCGCGTAACAAATAC  >  NC_000913/1081926‑1082192

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A