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
A5 F1 I2 R1	772	77.0	3769570	91.6%	3452926	105.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,214,757	T→C	Y571H (TAC→CAC)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,214,757	0	T	C	100.0%	133.2 / NA	38	Y571H (TAC→CAC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/24); total (14/24)

ACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCG  >  NC_000913/3214622‑3214891

accaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACcaca                                                                                                                                     >  1:1117192/1‑139 (MQ=255)

accaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACcaca                                                                                                                                     >  1:262750/1‑139 (MQ=255)

 ccaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  1:1785173/139‑1 (MQ=255)

  caccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACg                                                                                                                                   <  2:709176/139‑1 (MQ=255)

   accCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCTCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGc                                                                                                                                  <  2:1137125/139‑1 (MQ=255)

          aGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGgaaga                                                                                                                           <  1:1037338/139‑1 (MQ=255)

          aGCTGCCGCTGGATTCTGCGACAACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGgaaga                                                                                                                           <  1:1119529/139‑1 (MQ=255)

              gCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  2:1216432/126‑1 (MQ=255)

              gCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    >  1:1216432/1‑126 (MQ=255)

                    ggATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTaaa                                                                                                                 <  2:262750/139‑1 (MQ=255)

                    ggATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTaaa                                                                                                                 <  2:1351387/139‑1 (MQ=255)

                         cTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGaagaag                                                                                                                         >  1:510454/1‑126 (MQ=255)

                         cTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGaagaag                                                                                                                         <  2:510454/126‑1 (MQ=255)

                                caccGAAAGCCTGTGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGtt                                                                                                     >  2:1303520/1‑139 (MQ=255)

                                caccGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGtt                                                                                                     <  2:1248308/139‑1 (MQ=255)

                                    gAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAccc                                                                                                 <  1:8161/139‑1 (MQ=255)

                                        gCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  2:623304/139‑1 (MQ=255)

                                        gCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  1:775646/139‑1 (MQ=255)

                                            gcgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGt                                                                                         >  1:1706301/1‑139 (MQ=255)

                                             tgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        <  1:1303520/138‑1 (MQ=255)

                                             cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGTGTTTCGGTATCGATATGAACACTGACCacac                                                                                                                                    >  2:253270/1‑95 (MQ=255)

                                             cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGTGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  1:253270/95‑1 (MQ=255)

                                             cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        <  2:1766267/139‑1 (MQ=255)

                                             cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        >  2:1446223/1‑139 (MQ=255)

                                                                            tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCaa                                                         <  2:329207/139‑1 (MQ=255)

                                                                                    cgTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTc                                                 >  2:397068/1‑139 (MQ=255)

                                                                                           cAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAg                                          <  1:397068/139‑1 (MQ=255)

                                                                                                   cTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTg                                  <  2:1117192/139‑1 (MQ=255)

                                                                                                          tGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             >  1:1511169/1‑73 (MQ=255)

                                                                                                          tGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  2:1511169/73‑1 (MQ=255)

                                                                                                           gCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGtgctg                          >  2:515921/1‑139 (MQ=255)

                                                                                                                tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAAc                                                                                           <  1:983326/69‑1 (MQ=255)

                                                                                                                tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAAc                                                                                           >  2:983326/1‑69 (MQ=255)

                                                                                                                tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAg                     >  2:943629/1‑139 (MQ=255)

                                                                                                                            tGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGa         <  1:1446223/139‑1 (MQ=255)

                                                                                                                                cacCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGt                              >  2:1506670/1‑114 (MQ=255)

                                                                                                                                cacCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGt                              <  1:1506670/114‑1 (MQ=255)

                                                                                                                                   cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgc                                                                                               <  1:638817/46‑1 (MQ=255)

                                                                                                                                   cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgc                                                                                               >  2:638817/1‑46 (MQ=255)

                                                                                                                                   cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCg  >  2:1618837/1‑139 (MQ=255)

ACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCG  >  NC_000913/3214622‑3214891

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