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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,983,288	C→T	279 (TAG→TAA)	kduI ←	hexuronate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,983,288	0	C	T	100.0%	203.3 / NA	63	279 (TAG→TAA)	kduI	hexuronate isomerase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (29/34); total (29/34)

CAGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAACTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCACC  >  NC_000913/2983155‑2983417

caGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAgcg                                                                                                                              >  2:550430/1‑139 (MQ=255)

   cccGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCaa                                                                                                                           >  2:172057/1‑139 (MQ=255)

       cTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCt                                                                                                                       >  1:310549/1‑139 (MQ=255)

              cAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACgg                                                                                                                <  2:72360/139‑1 (MQ=255)

                  cccAACGCCATCCTCTGACCCAATCCAGTCTCACAACCAGTGCCGACCGCAACTTTACCATCCAGAGAAAATGCACTTAAACACAAAACAAAACCTTCTTTGTTTATGCCCCCAATTCTCGCAAAGCTTGAACGGCcac                                                                                                            <  2:476618/139‑1 (MQ=255)

                   ccAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           <  1:847883/139‑1 (MQ=255)

                   ccAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           <  1:550430/139‑1 (MQ=255)

                   ccAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACATTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           <  1:17811/139‑1 (MQ=255)

                            tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCttt                                                                                                                     <  1:138625/120‑1 (MQ=255)

                            tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCttt                                                                                                                     >  2:138625/1‑120 (MQ=255)

                            tCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCata                                                                                                  <  2:584011/139‑1 (MQ=255)

                                        gtccagtATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           <  2:1104228/118‑1 (MQ=255)

                                        gtccagtATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           >  1:1104228/1‑118 (MQ=255)

                                        gtccagtATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGAcc                                                                                      >  1:499903/1‑139 (MQ=255)

                                              tATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGttt                                                                                >  1:127525/1‑139 (MQ=255)

                                                  acaACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCAc                                                                            <  1:567918/139‑1 (MQ=255)

                                                   caACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGTCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCAcc                                                                           >  2:212887/1‑139 (MQ=255)

                                                     aCCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTcc                                                                                                     <  1:364790/111‑1 (MQ=255)

                                                     aCCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTcc                                                                                                     >  2:364790/1‑111 (MQ=255)

                                                        aGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCa                                                                                                    >  1:684244/1‑109 (MQ=255)

                                                        aGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCa                                                                                                    <  2:684244/109‑1 (MQ=255)

                                                        aGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCa                                                                      <  1:97423/139‑1 (MQ=255)

                                                         gTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCAt                                                                     <  1:485127/139‑1 (MQ=255)

                                                          tGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTaa                                                                                                                   <  1:228616/92‑1 (MQ=255)

                                                          tGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTaa                                                                                                                   >  2:228616/1‑92 (MQ=255)

                                                          tGACGACCGCAACTTTACCTTCGAGAG‑AAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGc                                                                   >  2:927239/1‑139 (MQ=255)

                                                            acgacCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGcc                                                                  <  1:1106301/139‑1 (MQ=255)

                                                             cgacCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGccc                                                                 <  2:499903/139‑1 (MQ=255)

                                                                              tCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGc                                                >  1:539272/1‑139 (MQ=255)

                                                                                     aaaaTGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGtt                                         >  2:941047/1‑139 (MQ=255)

                                                                                       aaTGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTcc                                       <  2:1111180/139‑1 (MQ=255)

                                                                                           cACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGaca                                   <  1:927239/139‑1 (MQ=255)

                                                                                           cACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAATTAGCACAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGaca                                   <  1:172057/139‑1 (MQ=255)

                                                                                                           aaTACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGAcc                   <  2:539272/139‑1 (MQ=255)

                                                                                                             tACCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAg                 >  1:97664/1‑139 (MQ=255)

                                                                                                              aCCTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGc                <  2:97664/139‑1 (MQ=255)

                                                                                                               ccTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATa                                                           >  1:289366/1‑95 (MQ=255)

                                                                                                               ccTTATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATa                                                           <  2:289366/95‑1 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                            <  1:894317/43‑1 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcac                                                                                                            >  2:894317/1‑43 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCat                                                                                                   <  1:819729/52‑1 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCat                                                                                                   >  2:819729/1‑52 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCa                                                                      >  1:955666/1‑81 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCa                                                                      <  2:955666/81‑1 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGaca                                   >  1:147087/1‑116 (MQ=255)

                                                                                                                  tATTCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGaca                                   <  2:147087/116‑1 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGta                                                     >  2:52751/1‑96 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGta                                                     <  1:52751/96‑1 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCgggg          <  1:941047/139‑1 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCgggg          >  2:116849/1‑139 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCgggg          >  2:737590/1‑139 (MQ=255)

                                                                                                                    ttCGTTTATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCgggg          <  2:127525/139‑1 (MQ=255)

                                                                                                                       gTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           <  1:598058/39‑1 (MQ=255)

                                                                                                                       gTTTATGCCCACAATTAGCGCAAATCTTTAACGGCcaca                                                                                                           >  2:598058/1‑39 (MQ=38)

                                                                                                                         ttATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATa                                                           >  2:1045088/1‑85 (MQ=255)

                                                                                                                         ttATGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATa                                                           <  1:1045088/85‑1 (MQ=255)

                                                                                                                           aTGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAg                                                                                         <  1:498822/53‑1 (MQ=255)

                                                                                                                           aTGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAg                                                                                         >  2:498822/1‑53 (MQ=255)

                                                                                                                            tGCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCAcc  >  1:255003/1‑139 (MQ=255)

                                                                                                                             gCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATgg                          <  2:719981/114‑1 (MQ=255)

                                                                                                                             gCCCACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATgg                          >  1:719981/1‑114 (MQ=255)

                                                                                                                              cccACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGAc                                                                                       >  1:1085452/1‑52 (MQ=255)

                                                                                                                              cccACAATTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGAc                                                                                       <  2:1085452/52‑1 (MQ=255)

CAGCCCGCTTGCGCCAGCCCCAACGCCATCCCCTGACCCAGTCCAGTATCACAACCAGTGACGACCGCAACTTTACCTTCGAGAGAAAATGCACTTAAAATCATAACAATACCTTATTCGTTTATGCCCACAACTAGCGCAAATCTTTAACGGCCACATGGTCCATATCATCAAAGACCTGGTTTTCACCGACCATGCCCCAGATAAAGGTATAAGCTTTGGTTCCGACACCGGAATGGATCGACCAGCTCGGGGAGATCACC  >  NC_000913/2983155‑2983417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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