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 F108 I1 R1	11	40.8	1469306	91.3%	1341476	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,542	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,542	0	C	A	94.9%	91.4 / NA	41	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (2/0); new base A (16/21); total (19/22)
Fisher's exact test for biased strand distribution p-value = 2.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184405‑4184675

tgCGGTTTAACGCCGTTTCCAGTCTGGTGACAAGATGGTAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                  <  2:485033/142‑1 (MQ=255)

        aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACACCGGAAGACATAGTACTGAAACAGCTGGGCTTAcag                                                                                                                          >  2:1154/1‑141 (MQ=255)

          cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGATCGAAGATATGCCTTACGCTGAAAACCGTACGCCGGTGCACATCGTACTGCCCCCGCTCCGCGTCCCGtc                                                                                                                        >  2:76052/1‑143 (MQ=255)

              gTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                    <  1:69555/143‑1 (MQ=255)

               gatgcAGCCGGGGGACAAGAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                   <  1:245437/139‑1 (MQ=255)

                    aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGCTGTGCCTTACGCTGAAAACGGTACGCCGGTAGACATCGGACTGAACCTGCTGGGCGTACCGTCTCGTATGAAc                                                                                                              >  2:355561/1‑143 (MQ=255)

                     gCCTGGTGACAAGATGGCAGGTCATCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACCGTCCGACGGTCGACCTCGTCCTGCACCCGCTGGGCGCACCGCCTCCTATGAAcc                                                                                                             >  1:129326/1‑142 (MQ=255)

                                 gctgtgaGGTCGTCACGGTAACAAGGGTGTAATTGCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATcc                                                                                                 <  1:205795/137‑1 (MQ=255)

                                  aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGCACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                >  2:469234/1‑143 (MQ=255)

                                       agctcctcACGGCAACAAGGGTGTAATTTCTCAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                           <  2:243452/137‑1 (MQ=255)

                                       aGGTCGTCACGGTAACAAGGGGGGAATTTCTAAGATCAACCCGATCGAGTATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                           <  1:114387/143‑1 (MQ=255)

                                         gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGCCTCGTATAAAACTCGGTGAGATCCCCGAAAcc                                                                                         >  1:330595/1‑143 (MQ=255)

                                              cACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAATACGGTACGCTGGTAGTCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCt                                                                                    <  2:67419/143‑1 (MQ=255)

                                               aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGCGCGTACCGTCTCGTATGAACATCGGACAGATCCTCGAAACCCaacag                                                                                   >  2:494186/1‑139 (MQ=255)

                                                 ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACACCGGTCAGATCCTCGAAACCCACCAggg                                                                                 >  2:621601/1‑143 (MQ=255)

                                                  atAACCAGGGTGTAACTGCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTTCGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGt                                                                                <  1:207291/142‑1 (MQ=255)

                                                    aagaaGGGTGGAATTTCTAAGAGCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTAt                                                                              <  2:703989/140‑1 (MQ=255)

                                                            tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCTGGGGATCGCTGCGa                                                                      >  2:244632/1‑143 (MQ=255)

                                                            tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGa                                                                      >  2:511917/1‑143 (MQ=255)

                                                              ttaTTTTTAATATCTTCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                    <  2:634549/141‑1 (MQ=255)

                                                               aaTTTCTAAGATCAACCTTATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                   <  2:42700/143‑1 (MQ=255)

                                                               aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCTGTAGACATTGTTTTGGTCGAGCAGAGCGAACCGGCACGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                   <  2:268495/143‑1 (MQ=255)

                                                                 tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTACGAAAGGt                                                                 >  1:1784/1‑143 (MQ=255)

                                                                  ttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACATCGGTCAGATCCTCGAGACCCACCTGGGTCTGGATgagtttatat                                                                >  2:226799/1‑134 (MQ=255)

                                                                   tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCACCTGGGTATAGCTGCAAAAGatat                                                               >  2:680312/1‑143 (MQ=255)

                                                                    cTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCACGGATGAACATCGGTCAGATCCTCGAAACCCACCTCGGTATGGGTGCGAAAGGTATc                                                              >  1:336531/1‑143 (MQ=255)

                                                                     tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGAACCTCGGTCAAATCCTCGAAACCCACCTGGGTATGGCTGCGAAAAGTATCg                                                             >  2:473127/1‑143 (MQ=255)

                                                                     tAAGATCAACCCGATCGAAGATATGCCTTACGAGGAAAACGGTACGCCGGTAGACATCGTACCGAACCAGCCGGGCGTACAGACTCGTATGAACATCGGTCAGGTCCACGAAACCCCCCTCGGTACTGCTGCGAACGGTCTCg                                                             >  1:549395/1‑143 (MQ=255)

                                                                          tCAATCCGATAGAAGATATGCCTTACGATGACAACGGTACGCCGGTAGACATCGTACTGAACTAGCTGTGCGTACCGTCTCCTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                        <  1:205033/143‑1 (MQ=255)

                                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTGAGATCCTCGAAGCCCACCTGGGGATGCCTGCGAAAGGTATCGGCGActa                                                      >  1:373838/1‑141 (MQ=255)

                                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACAAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGagca                                                      >  1:262476/1‑140 (MQ=255)

                                                                               ccGATCGAAGATATGCCTTACGATGAGAACGGTGCGCCGGTAGACATCGTACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                                   <  1:715147/143‑1 (MQ=255)

                                                                                   tCGAAGATATGCCTTACGATGAAAACGGTACGCTGGTAGACATCGTACTGTACTAGTTGGGCGTAGCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                               <  2:356695/143‑1 (MQ=255)

                                                                                   tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                               <  2:112177/143‑1 (MQ=255)

                                                                                             gCCGTACGATGAAAACGGCACGCCGGTAGACATCGAACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                     <  1:42846/143‑1 (MQ=255)

                                                                                                               tACGCCGGGAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                   <  1:365935/143‑1 (MQ=255)

                                                                                                                       tAGTCATCGTACGGAACCAGTTGGGTGTACCGTCTCGTATGAACGTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTg           <  1:638324/143‑1 (MQ=255)

                                                                                                                             tcccaCTGACCCGGCTGGGCGTGCCGTCTCGTATGAACAGCGGTCAGATCCTCGAAGCCCGCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa     <  1:621601/139‑1 (MQ=255)

                                                                                                                              cGTACTGAACCAGCTGGGCGTACCGTCTCGTGTGGCCAGCACACAAAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt    <  2:689874/143‑1 (MQ=255)

                                                                                                                                tACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCACCGCCGTGGGGAAACAGCGGCAAGACGTCGCTCAACTGTGCGAGtta  >  2:3404/1‑142 (MQ=255)

                                                                                                                                caCTGAACCATCTGTGCGTACCGTCTCTTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc  <  2:405329/142‑1 (MQ=255)

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184405‑4184675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A