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 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,803,711	T→C	pseudogene (194/1476 nt)	arpB →	pseudogene, ankyrin repeats

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,803,711	0	T	C	100.0%	165.2 / NA	46	pseudogene (194/1476 nt)	arpB	pseudogene, ankyrin repeats
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/24); total (22/24)

TTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGTCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATGTCAGTC  >  NC_000913/1803578‑1803845

ttGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCt                                                                                                                                   <  2:649139/139‑1 (MQ=255)

            tCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGAcg                                                                                                                       <  2:155951/139‑1 (MQ=255)

              tGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGAcgcg                                                                                                                     <  2:78700/139‑1 (MQ=255)

              tGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGAcgcg                                                                                                                     <  1:542764/139‑1 (MQ=255)

                                     tGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCa                                                                                              <  2:19766/139‑1 (MQ=255)

                                       tCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCAtc                                                                                            <  1:433203/139‑1 (MQ=255)

                                        cATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCAtcc                                                                                           <  1:368072/139‑1 (MQ=255)

                                               aTACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGAcg                                                                                                                       <  1:708238/104‑1 (MQ=255)

                                               aTACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGAcg                                                                                                                       >  2:708238/1‑104 (MQ=255)

                                               aTACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCa                                                                                    >  2:274610/1‑139 (MQ=255)

                                                 aCGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCg                                                                                                                            <  2:856796/97‑1 (MQ=255)

                                                 aCGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCg                                                                                                                            >  1:856796/1‑97 (MQ=255)

                                                 aCGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACATGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAgg                                                                                  >  2:189863/1‑139 (MQ=255)

                                                   gCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGa                                                                                >  1:135083/1‑139 (MQ=255)

                                                     ccTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGtt                                                                                                                <  1:769164/105‑1 (MQ=255)

                                                     ccTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGtt                                                                                                                >  2:769164/1‑105 (MQ=255)

                                                     ccTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCa                                                                                              >  2:174369/1‑123 (MQ=255)

                                                     ccTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCa                                                                                              <  1:174369/123‑1 (MQ=255)

                                                     ccTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGt                                                                              >  1:618297/1‑139 (MQ=255)

                                                               ttGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATcg                                                                    <  2:250622/139‑1 (MQ=255)

                                                                                 aaaGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCt                                                  <  1:274610/139‑1 (MQ=255)

                                                                                 aaaGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCt                                                  <  1:189863/139‑1 (MQ=255)

                                                                                                       aCTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGGGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGCGTCGCGTTATCGCGCGTAAGGCTTTTGGCTTCGCTTTAGCTATTTCCTTTTg                            >  2:494419/1‑139 (MQ=255)

                                                                                                       aCTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCAtcc                                                                                           <  2:153770/76‑1 (MQ=255)

                                                                                                       aCTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCAtcc                                                                                           >  1:153770/1‑76 (MQ=255)

                                                                                                       aCTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTAt                                                                      >  2:510433/1‑97 (MQ=255)

                                                                                                       aCTCCTCCGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTAt                                                                      <  1:510433/97‑1 (MQ=255)

                                                                                                          cctccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCg                         >  1:727624/1‑139 (MQ=255)

                                                                                                           ctccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCt                                                  >  1:768941/1‑113 (MQ=255)

                                                                                                           ctccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCt                                                  <  2:768941/113‑1 (MQ=255)

                                                                                                           ctccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGa                        >  2:131111/1‑139 (MQ=255)

                                                                                                            tccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGc                                                                                                          >  2:296223/1‑56 (MQ=255)

                                                                                                            tccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGc                                                                                                          <  1:296223/56‑1 (MQ=255)

                                                                                                             ccGTTGAATCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAat                      >  2:544887/1‑139 (MQ=255)

                                                                                                              cGTTGAATCCATACAGCAGCATGCCCCATTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAatg                     >  2:45407/1‑139 (MQ=255)

                                                                                                                    acagaTACAGCCGCATGGCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCa               <  2:476228/135‑1 (MQ=255)

                                                                                                                    aTCCATACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCa               <  2:116746/139‑1 (MQ=255)

                                                                                                                        aTACAGCAGTATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTGGTCGAATGATGGCAAACa           >  1:624759/1‑139 (MQ=255)

                                                                                                                        aTACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATcg                                                                    >  2:579555/1‑82 (MQ=255)

                                                                                                                        aTACAGCAGCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATcg                                                                    <  1:579555/82‑1 (MQ=255)

                                                                                                                           cagcagCATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATg        <  1:544887/139‑1 (MQ=255)

                                                                                                                            agcagcATGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATgt       <  2:727624/139‑1 (MQ=255)

                                                                                                                             gcagcaTGCCCCATTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATgtc      <  1:45407/139‑1 (MQ=255)

                                                                                                                                gcaTGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATgtcagt   >  2:921628/1‑139 (MQ=255)

                                                                                                                                 caTGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGTAAACAATgtcagtc  >  1:220271/1‑139 (MQ=255)

                                                                                                                                 caTGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATgt       >  2:497988/1‑134 (MQ=255)

                                                                                                                                 caTGCCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATgt       <  1:497988/134‑1 (MQ=255)

TTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAATCCATACAGCAGCATGTCCCCTTAGTCCGGGACGCGGAGTTCAGAGCATTACTTCGCCATCCTCCTGCAGGGAGTCGCGTTATCGCGAGTAAGGATTTTGGCTTCGCTTTAGATATTTTCTTTTGTCGAATGATGGCAAACAATGTCAGTC  >  NC_000913/1803578‑1803845

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