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
A10 F73 I1 R1	26	53.7	1833324	99.1%	1816824	139.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,464,116	C→A	S65S (TCC→TCA)	gspL →	Type II secretion system protein GspL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,464,116	0	C	A	96.2%	170.9 / 0.4	52	S65S (TCC→TCA)	gspL	Type II secretion system protein GspL
Reads supporting (aligned to +/- strand): ref base C (1/1); new base A (20/30); total (21/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

TGGATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCCCTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGTTGTCGATAAACAAAACGAAAGTGTCGAGGT  >  NC_000913/3463979‑3464247

tGGATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACt                                                                                                                                   >  1:152649/1‑140 (MQ=255)

 ggATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTc                                                                                                                                  >  2:703350/1‑140 (MQ=255)

 ggATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTc                                                                                                                                  >  1:876695/1‑140 (MQ=255)

 ggATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTc                                                                                                                                  >  1:608138/1‑140 (MQ=255)

  gATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCa                                                                                                                                 >  1:35761/1‑140 (MQ=255)

    tGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACg                                                                                                                               >  2:9539/1‑140 (MQ=255)

     gACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGc                                                                                                                              <  1:34854/140‑1 (MQ=255)

       cGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTg                                                                                                                            >  2:533798/1‑140 (MQ=255)

          tctcCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGccc                                                                                                                         <  1:649441/140‑1 (MQ=255)

           ctcCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCa                                                                                                                        <  1:141941/140‑1 (MQ=255)

               gCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGc                                                                                                                    <  2:599122/140‑1 (MQ=255)

                 aGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCa                                                                                                                  <  1:489550/140‑1 (MQ=255)

                 aGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCa                                                                                                                  <  1:281710/140‑1 (MQ=255)

                 aGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCa                                                                                                                  <  1:9539/140‑1 (MQ=255)

                  gATAGCGTATCTTCGGCACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTCTTATATCGTTCACTCACGCTGCCCAACGCCaa                                                                                                                 >  2:426990/1‑140 (MQ=255)

                        gTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCCCTCACGCTGCCCAACGCCAAATACaa                                                                                                           >  1:204354/1‑140 (MQ=255)

                              tCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCAc                                                                                                     <  1:559439/140‑1 (MQ=255)

                                 gTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGc                                                                                                  >  1:290805/1‑140 (MQ=255)

                                 gTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGc                                                                                                  <  2:24009/140‑1 (MQ=255)

                                 gTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGc                                                                                                  >  2:485062/1‑140 (MQ=255)

                                    cATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGcaca                                                                                               <  1:814316/140‑1 (MQ=255)

                                    cATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGcaca                                                                                               <  1:634172/140‑1 (MQ=255)

                                     aTACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACaa                                                                                              >  2:440559/1‑140 (MQ=255)

                                      tACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACaaa                                                                                             <  1:169043/140‑1 (MQ=255)

                                        cGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACa                                                                                           <  2:166799/140‑1 (MQ=255)

                                           tCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCCCCGCACAAACATTa                                                                                        >  2:570032/1‑140 (MQ=255)

                                            cACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTAc                                                                                       >  2:63368/1‑140 (MQ=255)

                                            cACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTAc                                                                                       >  2:169232/1‑140 (MQ=255)

                                             aCGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACa                                                                                      <  2:290805/140‑1 (MQ=255)

                                              cGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACaa                                                                                     >  1:116260/1‑140 (MQ=255)

                                                 aCGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAAtgg                                                                                  <  1:95894/140‑1 (MQ=255)

                                                     tCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAAtggctgg                                                                              <  2:152649/140‑1 (MQ=255)

                                                     tCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAAtggctgg                                                                              <  1:440559/140‑1 (MQ=255)

                                                     tCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAAtggctgg                                                                              <  2:591253/140‑1 (MQ=255)

                                                             tGGAGTCGCTGGCCGATCGGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAgaggag                                                                      >  2:651135/1‑140 (MQ=255)

                                                               gAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGAc                                                                    >  2:855508/1‑140 (MQ=255)

                                                                        gCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGa                                                           <  2:555439/140‑1 (MQ=255)

                                                                          cGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGaca                                                         <  1:703350/140‑1 (MQ=255)

                                                                           gATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGacaa                                                        <  1:169232/140‑1 (MQ=255)

                                                                                gCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCCCTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACAccc                                                   <  2:204354/140‑1 (MQ=255)

                                                                                     gTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGAc                                              <  2:876695/140‑1 (MQ=255)

                                                                                     gTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGAc                                              <  1:485062/140‑1 (MQ=255)

                                                                                      tGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACt                                             >  2:651334/1‑140 (MQ=255)

                                                                                        ccGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTgg                                           <  2:33036/140‑1 (MQ=255)

                                                                                         cGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGc                                          >  2:409552/1‑140 (MQ=255)

                                                                                           gAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCa                                         <  1:14576/139‑1 (MQ=255)

                                                                                           gAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCa                                         >  2:14576/1‑139 (MQ=255)

                                                                                               tGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGa                                    <  2:608138/140‑1 (MQ=255)

                                                                                               tGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGa                                    <  1:855508/140‑1 (MQ=255)

                                                                                                   cATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCTCAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGt                                <  2:116260/140‑1 (MQ=255)

                                                                                                           gATCCCACCAGAGGGCCTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGTTGTCGATa                        <  1:694048/140‑1 (MQ=255)

                                                                                                                           cTTTTATATCGTTCACTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGTTGTCGATAAACAAAACGAAAgtgt        >  2:514105/1‑140 (MQ=255)

                                                                                                                                 tatCGTTCACTCACGCTGCCCAACGCCGAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGTTGTCGATAAACAAAACGAAAGTGTCGAGGt  <  2:248618/140‑1 (MQ=255)

TGGATGACGTTCTCCGCAGATAGCGTATCTTCGGTACATACGCTCACGGACGATCTTCCGCTGGAGTCGCTGGCCGATCAGCCCGGTGCCGGAAATGTTCATCTTTTGATCCCACCAGAGGGCCTTTTATATCGTTCCCTCACGCTGCCCAACGCCAAATACAAACTCACCGCACAAACATTACAATGGCTGGCAGAGGAGACGTTACCCGACAACACCCAGGACTGGCACTGGACGGTTGTCGATAAACAAAACGAAAGTGTCGAGGT  >  NC_000913/3463979‑3464247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A