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	77	34.8	1608548	95.0%	1528120	114.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,504,515	C→T	R267C (CGC→TGC)	insQ →	IS609 transposase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,504,515	0	C	T	93.5%	86.5 / ‑1.2	31	R267C (CGC→TGC)	insQ	IS609 transposase B
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (15/14); total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

CAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTAT  >  NC_000913/1504384‑1504643

cAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGt                                                                                                                           >  1:283281/1‑139 (MQ=255)

           aGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAAt                                                                                                                <  2:525265/139‑1 (MQ=255)

                       cacaAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAAcc                                                                                                    >  2:789403/1‑139 (MQ=255)

                       cacaAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAAcc                                                                                                    >  2:763481/1‑139 (MQ=255)

                         caAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGt                                                                                                  >  2:408738/1‑139 (MQ=255)

                          aaaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                 <  1:789403/139‑1 (MQ=255)

                           aaGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTc                                                                                                <  2:569488/139‑1 (MQ=255)

                              tCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGa                                                                                              <  1:312296/138‑1 (MQ=255)

                              tCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGa                                                                                              >  2:312296/1‑138 (MQ=255)

                              tCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGAt                                                                                             >  1:586702/1‑139 (MQ=255)

                               cacaACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATa                                                                                            <  1:367940/139‑1 (MQ=255)

                                 caACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACt                                                                                          >  2:595909/1‑139 (MQ=255)

                                   aCGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTgg                                                                                        >  2:311338/1‑139 (MQ=255)

                                      gCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATc                                                                                     >  2:91479/1‑139 (MQ=255)

                                          tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                 <  1:239272/123‑1 (MQ=255)

                                          tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                 >  2:239272/1‑123 (MQ=255)

                                          tCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                 <  1:408738/139‑1 (MQ=255)

                                                        gCAATGATAGTCATTGAGGATTTGAAGGTAAGCAACATGTCAAAGACAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATgc                                                                   >  1:462950/1‑139 (MQ=255)

                                                                  tCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCt                                                         <  1:91479/139‑1 (MQ=255)

                                                                                             tGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                 >  2:185701/1‑72 (MQ=255)

                                                                                             tGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGtt                                                                                                 <  1:185701/72‑1 (MQ=255)

                                                                                              gTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGt                             <  2:381074/139‑1 (MQ=255)

                                                                                                       agcagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTa                                                                                                        <  2:350213/55‑1 (MQ=255)

                                                                                                       agcagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTa                                                                                                        >  1:350213/1‑55 (MQ=255)

                                                                                                       agcagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGtgctt                    <  2:283281/139‑1 (MQ=255)

                                                                                                        gcagcGGGTACGGTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGtgcttg                   >  2:126646/1‑139 (MQ=255)

                                                                                                                   ggTCAGCCAGCCGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCa        <  1:675723/139‑1 (MQ=255)

                                                                                                                   ggTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCa        <  1:311338/139‑1 (MQ=255)

                                                                                                                         ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                 <  1:87138/60‑1 (MQ=255)

                                                                                                                         ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAggg                                                                                 >  2:87138/1‑60 (MQ=255)

                                                                                                                         ccagccGGGGTGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGTGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGtat  >  1:308993/1‑139 (MQ=255)

CAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGCGTATAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTAT  >  NC_000913/1504384‑1504643

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