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	69	53.0	2252012	96.1%	2164183	115.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,467,061	C→T	pseudogene (1670/2513 nt)	ydbA →	pseudogene, autotransporter homolog, interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,467,061	0	C	T	100.0%	169.6 / NA	49	pseudogene (1670/2513 nt)	ydbA	pseudogene, autotransporter homolog, interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/29); total (20/29)

CAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTG  >  NC_000913/1466925‑1467186

cAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgtgc                                                                                                                             <  2:774087/139‑1 (MQ=255)

 aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCa                                                                                                                            <  2:234827/139‑1 (MQ=255)

        cGGTAACGACGCCACCGCGAATAACAATGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATg                                                                                                                          <  1:121417/134‑1 (MQ=255)

        cGGTAACGACGCCACCGCGAATAACAATGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATg                                                                                                                          >  2:121417/1‑134 (MQ=255)

           tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTgag                                                                                                                  <  2:313228/139‑1 (MQ=255)

            aaCGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGTGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTgaga                                                                                                                 <  2:871684/139‑1 (MQ=255)

             acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGaa                                                                                                                >  2:327782/1‑139 (MQ=255)

                 cgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACAtt                                                                                                            >  2:237872/1‑139 (MQ=255)

                  gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTg                                                                                                           >  2:186406/1‑139 (MQ=255)

                  gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACAAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTg                                                                                                           >  2:602087/1‑139 (MQ=255)

                            aTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACgg                                                                                                 <  1:162057/139‑1 (MQ=255)

                              aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  2:363290/139‑1 (MQ=255)

                                         aaCCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaac                                                                                    <  1:359692/139‑1 (MQ=255)

                                            cACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACaaa                                                                                 <  2:961082/139‑1 (MQ=255)

                                             aCTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:633299/124‑1 (MQ=255)

                                             aCTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:633299/1‑124 (MQ=255)

                                                   gATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:145519/118‑1 (MQ=255)

                                                   gATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:145519/1‑118 (MQ=255)

                                                    aTGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGatat                                                                         >  1:1036726/1‑139 (MQ=255)

                                                         aaaGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgttg                                                                    <  1:237872/139‑1 (MQ=255)

                                                           aGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTgttgtt                                                                  >  2:328354/1‑139 (MQ=255)

                                                             aTTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                <  2:685425/139‑1 (MQ=255)

                                                                                 gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGa                                                                                                       >  1:575459/1‑80 (MQ=255)

                                                                                 gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGa                                                                                                       <  2:575459/80‑1 (MQ=255)

                                                                                 gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCg                                            <  1:572261/139‑1 (MQ=255)

                                                                                 gcgGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCg                                            <  1:881515/139‑1 (MQ=255)

                                                                                      cAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCtc                                       <  2:196149/139‑1 (MQ=255)

                                                                                                    tAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAggg                         >  1:166342/1‑139 (MQ=255)

                                                                                                     aaaTCTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAgggg                        <  2:46201/139‑1 (MQ=255)

                                                                                                         cTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCaa                    <  2:582750/139‑1 (MQ=255)

                                                                                                         cTGGATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCaa                    <  1:76446/139‑1 (MQ=255)

                                                                                                            gATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               >  2:288146/1‑61 (MQ=255)

                                                                                                            gATGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCa                                                                                               <  1:288146/61‑1 (MQ=255)

                                                                                                              tGGTAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTa               >  1:1079610/1‑139 (MQ=255)

                                                                                                                 tAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACa                                                                                                              >  2:74583/1‑41 (MQ=255)

                                                                                                                 tAGCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACa                                                                                                              <  1:74583/41‑1 (MQ=255)

                                                                                                                   gCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCaa          >  1:551021/1‑139 (MQ=255)

                                                                                                                   gCCTGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCaa          >  1:242495/1‑139 (MQ=255)

                                                                                                                      tGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                <  1:85553/82‑1 (MQ=255)

                                                                                                                      tGACTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc                                                                >  2:85553/1‑82 (MQ=255)

                                                                                                                         cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  1:328354/139‑1 (MQ=255)

                                                                                                                         cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  1:602087/139‑1 (MQ=255)

                                                                                                                         cTGTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  2:1079610/139‑1 (MQ=255)

                                                                                                                           gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATc             <  2:290097/128‑1 (MQ=255)

                                                                                                                           gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATc             >  1:290097/1‑128 (MQ=255)

                                                                                                                           gTTACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTg  <  1:924166/139‑1 (MQ=255)

                                                                                                                             tACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    <  2:372484/135‑1 (MQ=255)

                                                                                                                             tACAGGCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACggg    >  1:372484/1‑135 (MQ=255)

                                                                                                                                  gCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaa                                                                                     >  2:594140/1‑49 (MQ=255)

                                                                                                                                  gCGGTGTGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaa                                                                                     <  1:594140/49‑1 (MQ=255)

CAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATACTGGATCGATTGGCGTGCTCATCAACGGTGAGGGGGCAACAGTATCCAATACGGGTG  >  NC_000913/1466925‑1467186

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A