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
A4 F1 I2 R1	780	68.3	3343050	93.5%	3125751	102.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,500,043	C→T	pseudogene (492/942 nt)	yjgX ←	pseudogene fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,500,043	0	C	T	100.0%	172.5 / NA	54	pseudogene (492/942 nt)	yjgX	pseudogene fragment
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (27/27); total (27/27)

TAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAAC  >  NC_000913/4499912‑4500151

tAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGt                                                                                                       >  1:1253591/1‑139 (MQ=255)

       tGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCt                                                                                                >  1:334956/1‑139 (MQ=255)

       tGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATAATTCGGTTAGGAGTTAAGGCt                                                                                                >  1:1232448/1‑139 (MQ=255)

        ggCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTGGGAGTTAAGGCTg                                                                                               <  2:570189/139‑1 (MQ=255)

        ggCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTg                                                                                               <  2:1544026/139‑1 (MQ=255)

          cGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGtt                                                                                             >  1:753765/1‑138 (MQ=255)

             aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                          <  2:753765/139‑1 (MQ=255)

             aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                          <  2:334956/139‑1 (MQ=255)

               tGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACg                                                                                        >  1:769410/1‑139 (MQ=255)

                   gTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGAtt                                                                                    >  2:324130/1‑139 (MQ=255)

                      aGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTgg                                                                                 >  1:511252/1‑139 (MQ=255)

                       gTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGa                                                                                <  1:324130/139‑1 (MQ=255)

                        tACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                               <  2:511252/139‑1 (MQ=255)

                        tACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                               <  2:535229/139‑1 (MQ=255)

                          ccGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATga                                                                             >  2:1363152/1‑139 (MQ=255)

                                aaGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAccc                                                                       >  1:566534/1‑139 (MQ=255)

                                        cATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGAttt                                                                                   <  2:1460521/119‑1 (MQ=255)

                                        cATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGAttt                                                                                   >  1:1460521/1‑119 (MQ=255)

                                          tCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTa                                                                                                            >  1:1349293/1‑92 (MQ=255)

                                              gCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTg                                                                                               <  2:1307311/101‑1 (MQ=255)

                                              gCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTg                                                                                               >  1:1307311/1‑101 (MQ=255)

                                                  gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         <  1:1614932/119‑1 (MQ=255)

                                                  gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         >  2:1614932/1‑119 (MQ=255)

                                                      aGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCt                                                 <  2:1232448/139‑1 (MQ=255)

                                                            ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         <  2:457324/109‑1 (MQ=255)

                                                            ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         >  1:457324/1‑109 (MQ=255)

                                                               tCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                        <  1:1363152/139‑1 (MQ=255)

                                                               tCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                        <  2:1253591/139‑1 (MQ=255)

                                                                      tACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                            <  2:55489/128‑1 (MQ=255)

                                                                      tACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                            >  1:55489/1‑128 (MQ=255)

                                                                      tACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATc                                 >  1:607092/1‑139 (MQ=255)

                                                                              cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                         <  1:864736/75‑1 (MQ=255)

                                                                              cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                         >  2:864736/1‑75 (MQ=255)

                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTa                                                                                                            >  1:874112/1‑54 (MQ=255)

                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCAtgtg                                                               >  1:306278/1‑99 (MQ=255)

                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCAtgtg                                                               <  2:306278/99‑1 (MQ=255)

                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                        <  2:61229/122‑1 (MQ=255)

                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                        >  1:61229/1‑122 (MQ=255)

                                                                                   gAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                    <  2:607092/139‑1 (MQ=255)

                                                                                       tAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATc                                                  >  2:497757/1‑105 (MQ=255)

                                                                                       tAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATc                                                  <  1:497757/105‑1 (MQ=255)

                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgtg                                                                            <  1:1003022/70‑3 (MQ=255)

                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                            >  2:1003022/1‑70 (MQ=255)

                                                                                                  ttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAgg                                                                                                  >  1:1170111/1‑46 (MQ=255)

                                                                                                  ttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAgg                                                                                                  <  2:1170111/46‑1 (MQ=255)

                                                                                                     tCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTaacaac  <  2:890334/139‑1 (MQ=255)

                                                                                                                    cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                         >  1:1456698/1‑37 (MQ=255)

                                                                                                                    cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                         <  2:1456698/37‑1 (MQ=255)

                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         >  1:1528934/1‑51 (MQ=255)

                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAAc                                                                         <  2:1528934/51‑1 (MQ=255)

                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGcc                             <  1:1006309/95‑1 (MQ=255)

                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGcc                             >  2:1006309/1‑95 (MQ=255)

                                                                                                                              ttCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                            <  1:98383/40‑1 (MQ=255)

                                                                                                                              ttCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                            >  2:98383/1‑40 (MQ=255)

TAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAAC  >  NC_000913/4499912‑4500151

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