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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	668,430	G→A	R96C (CGC→TGC)	rlmH ←	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	668,430	0	G	A	87.9%	75.7 / 4.2	33	R96C (CGC→TGC)	rlmH	23S rRNA m(3)Psi1915 pseudouridine methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (14/15); total (16/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01

TCTGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTCACCCTCTTTGTCGAGTA  >  NC_000913/668303‑668561

tctGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCt                                                                                                                          >  1:636326/1‑139 (MQ=255)

        cAGCACGCGAACCAACGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACACGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGt                                                                                                                  >  1:652726/1‑139 (MQ=255)

          gCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTc                                                                                                                >  2:926719/1‑139 (MQ=255)

                 aaCCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCa                                                                                                         <  2:795654/139‑1 (MQ=255)

                            gggggAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTg                                                                                              <  2:584638/139‑1 (MQ=255)

                                 aGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTgcggcg                                                                                         <  2:721804/139‑1 (MQ=255)

                                 aGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTgcggcg                                                                                         <  2:652726/139‑1 (MQ=255)

                                 aGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTgcggcg                                                                                         <  2:563239/139‑1 (MQ=255)

                                    gTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTgcggcg                                                                                         <  2:831544/136‑1 (MQ=255)

                                    gTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTgcggcg                                                                                         >  1:831544/1‑136 (MQ=255)

                                        gcgcCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCa                                                                                  >  1:228306/1‑139 (MQ=255)

                                                aGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGc                                                                          <  1:12560/139‑1 (MQ=255)

                                                aGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGc                                                                          <  1:658647/139‑1 (MQ=255)

                                                    aCCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTgg                                                                      >  2:1015086/1‑139 (MQ=255)

                                                        gCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAata                                                                  <  2:228306/139‑1 (MQ=255)

                                                               tCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAggg                                                           <  1:1015086/139‑1 (MQ=255)

                                                                  gccgccGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGa                                                        <  2:409721/139‑1 (MQ=255)

                                                                   ccgccgCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGAc                                                       >  1:1041045/1‑139 (MQ=255)

                                                                   ccgccgCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTcc                                                                                                                       >  2:416169/1‑75 (MQ=255)

                                                                   ccgccgCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTcc                                                                                                                       <  1:416169/75‑1 (MQ=255)

                                                                   ccgccgCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCt                                                                                                   >  2:15974/1‑95 (MQ=255)

                                                                   ccgccgCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCt                                                                                                   <  1:15974/95‑1 (MQ=255)

                                                                                      cGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGc                                                                              >  1:982775/1‑97 (MQ=255)

                                                                                      cGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGc                                                                              <  2:982775/97‑1 (MQ=255)

                                                                                            cccTTCAGGCCCGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGgccgcc                              <  1:926719/139‑1 (MQ=255)

                                                                                                       cGCCAATCAGTAGACTGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTc                   >  1:67631/1‑139 (MQ=255)

                                                                                                                      tGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGc                                                                              >  2:604089/1‑65 (MQ=255)

                                                                                                                      tGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGc                                                                              <  1:604089/65‑1 (MQ=255)

                                                                                                                      tGACGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTCACCCTCTTTGTCGAg    >  2:273303/1‑139 (MQ=255)

                                                                                                                        aCGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTCACCCTCTTTGTCGAGTa  >  2:381294/1‑139 (MQ=255)

                                                                                                                        aCGTCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTCACCCTCTTTGTCGAGTa  >  1:85432/1‑139 (MQ=255)

                                                                                                                           tCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAAc                           >  2:495263/1‑111 (MQ=255)

                                                                                                                           tCGCAACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAAc                           <  1:495263/111‑1 (MQ=255)

TCTGCGACCAGCACGCGAACCAGCGGATGGGGGAGGGTAAGCGCCGACAGCGACCAGCTCTGCTCAGCCGCCGCTTTACAGGCAGGCGACAACCCTTCAGGCCCGCCAATCAGTAGACTGACGTCGCGACCATCCAGCTTCCAGCGTTCCAGCTCAGCGGCTAACTGCGGCGTATCCCAGGGCTTGCCTGGAATATCGAGGGTGACAATGCGGTTTTTGCCTGCGGCCGCCAACATCTGCTCACCCTCTTTGTCGAGTA  >  NC_000913/668303‑668561

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A